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Page 1: The Website was developed thanks to the

The Website was developed thanks to the collaboration between MEDINFO laboratory of DIST and Giannina Gaslini Pediatric Hospital in

order to create a user friendly scientific consultation web tool

Giannina GasliniInstitute staff uses Proteome LabTMPF2D by Beckman Coulter (Milan Italy) in order to obtain chromatography and to separate molecules (proteins e polypeptides) contained in serum

Thanks to Microsoft SQL Server 2008 Visual Studio 2008 and web services we developed a website that allows us to search and display information about proteins detected by Gaslini Institute through chromatography

bull Itrsquos the study of the set of proteins expressed by a certain tissue or organism in a determined momentbull This discipline studies the proteome the set of proteins of an organism or a biological system (Mark Wilkins 1994)

techniques (separation and identification of proteins analysis of proteins sequence etchellip)

identification of a marker or a peptide markers pattern useful for the clinical diagnosis of a pathology

Many databases (IPI UniProtKB EMBL Nucleotide Sequence Database

Ensembl) contain information about proteins obtained directly by laboratory

experiments or by scientific literature

Web Services Choreography In order to organize understand and

better use of the knowledge

A Web Service as defined by W3C is a software system designed for the interoperability between different elaborators connected by the same network

Web services can be combined (choreography) in order to solve the problem of information integration between the databases in a functional and repeatable process

Web services standardize the mechanisms by which different machines can interact giving some services

They respond to HTTP requests formatted by SOAP syntax

SOAP (Simple Object Access Protocol) is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks and underlies the Web Services message protocol

This protocol is based on XML meta-language

WSDL is a document based on XML which contains a set of definitions that permits to specify web service features

ltwsdldefinitionsxmlnssoapenc=httpschemasxmlsoaporgsoapencoding xmlnsapachesoap=httpxmlapacheorgxml-soap xmlnstns1=httpexceptionsjdbfetchebiacuk xmlnswsdlsoap=httpschemasxmlsoaporgwsdlsoap xmlnsxsd=httpwwww3org2001XMLSchema xmlnsimpl=httpwwwebiacukwsservicesWSDbfetch xmlnsintf=httpwwwebiacukwsservicesWSDbfetch targetNamespace=httpwwwebiacukwsservicesWSDbfetch xmlnswsdl=httpschemasxmlsoaporgwsdlgt

ID HEMO_HUMAN Reviewed 462 AAAC P02790 B2R957DT 21-JUL-1986 integrated into UniProtKBSwiss-ProtDT 01-OCT-1996 sequence version 2DT 10-FEB-2009 entry version 99DE RecName Full=HemopexinDE AltName Full=Beta-1B-glycoproteinDE Flags PrecursorGN Name=HPXOS Homo sapiens (Human)OC Eukaryota Metazoa Chordata Craniata Vertebrata EuteleostomiOC Mammalia Eutheria Euarchontoglires Primates HaplorrhiniOC Catarrhini Hominidae HomoOX NCBI_TaxID=9606helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphellipCC -- FUNCTION Binds heme and transports it to the liver for breakdownCC and iron recovery after which the free hemopexin returns to theCC circulationCcCC -- SUBUNIT Interacts with HEV ORF3 proteinCC -- SUBCELLULAR LOCATION SecretedCC -- TISSUE SPECIFICITY Expressed by the liver and secreted in plasmahelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

hellipDR GO GO0005615 Cextracellular space TASProtIncDR GO GO0015232 Fheme transporter activity TASProtIncDR GO GO0005506 Firon ion binding IEAUniProtKB-KWDR GO GO0006879 Pcellular iron ion homeostasis TASProtIncDR GO GO0015886 Pheme transport TASProtIncDR GO GO0044419 Pinterspecies interaction between organisms IEAUniProtKB-KWhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipSQ SEQUENCE 462 AA 51676 MW 054B44D0603763B8 CRC64 MARVLGAPVA LGLWSLCWSL AIATPLPPTS AHGNVAEGET KPDPDVTERC SDGWSFDATT

LDDNGTMLFF KGEFVWKSHK WDRELISERW KNFPSPVDAA FRQGHNSVFL IKGDKVWVYP PEKKEKGYPK LLQDEFPGIP SPLDAAVECH RGECQAEGVL FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC FQGNQFLRFD PVRGEVPPRY PRDVRDYFMP CPGRGHGHRN GTGHGNSTHH GPEYMRCSPH LVLSALTSDN HGATYAFSGT HYWRLDTSRD GWHSWPIAHQ WPQGPSAVDA AFSWEEKLYL VQGTQVYVFL TKGGYTLVSG YPKRLEKEVG TPHGIILDSV DAAFICPGSSRLHIMAGRRL WWLDLKSGAQ ATWTELPWPH EKVDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE KLNAAKALPQ PQNVTSLLGC TH

Extractable features

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 2: The Website was developed thanks to the

Giannina GasliniInstitute staff uses Proteome LabTMPF2D by Beckman Coulter (Milan Italy) in order to obtain chromatography and to separate molecules (proteins e polypeptides) contained in serum

Thanks to Microsoft SQL Server 2008 Visual Studio 2008 and web services we developed a website that allows us to search and display information about proteins detected by Gaslini Institute through chromatography

bull Itrsquos the study of the set of proteins expressed by a certain tissue or organism in a determined momentbull This discipline studies the proteome the set of proteins of an organism or a biological system (Mark Wilkins 1994)

techniques (separation and identification of proteins analysis of proteins sequence etchellip)

identification of a marker or a peptide markers pattern useful for the clinical diagnosis of a pathology

Many databases (IPI UniProtKB EMBL Nucleotide Sequence Database

Ensembl) contain information about proteins obtained directly by laboratory

experiments or by scientific literature

Web Services Choreography In order to organize understand and

better use of the knowledge

A Web Service as defined by W3C is a software system designed for the interoperability between different elaborators connected by the same network

Web services can be combined (choreography) in order to solve the problem of information integration between the databases in a functional and repeatable process

Web services standardize the mechanisms by which different machines can interact giving some services

They respond to HTTP requests formatted by SOAP syntax

SOAP (Simple Object Access Protocol) is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks and underlies the Web Services message protocol

This protocol is based on XML meta-language

WSDL is a document based on XML which contains a set of definitions that permits to specify web service features

ltwsdldefinitionsxmlnssoapenc=httpschemasxmlsoaporgsoapencoding xmlnsapachesoap=httpxmlapacheorgxml-soap xmlnstns1=httpexceptionsjdbfetchebiacuk xmlnswsdlsoap=httpschemasxmlsoaporgwsdlsoap xmlnsxsd=httpwwww3org2001XMLSchema xmlnsimpl=httpwwwebiacukwsservicesWSDbfetch xmlnsintf=httpwwwebiacukwsservicesWSDbfetch targetNamespace=httpwwwebiacukwsservicesWSDbfetch xmlnswsdl=httpschemasxmlsoaporgwsdlgt

ID HEMO_HUMAN Reviewed 462 AAAC P02790 B2R957DT 21-JUL-1986 integrated into UniProtKBSwiss-ProtDT 01-OCT-1996 sequence version 2DT 10-FEB-2009 entry version 99DE RecName Full=HemopexinDE AltName Full=Beta-1B-glycoproteinDE Flags PrecursorGN Name=HPXOS Homo sapiens (Human)OC Eukaryota Metazoa Chordata Craniata Vertebrata EuteleostomiOC Mammalia Eutheria Euarchontoglires Primates HaplorrhiniOC Catarrhini Hominidae HomoOX NCBI_TaxID=9606helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphellipCC -- FUNCTION Binds heme and transports it to the liver for breakdownCC and iron recovery after which the free hemopexin returns to theCC circulationCcCC -- SUBUNIT Interacts with HEV ORF3 proteinCC -- SUBCELLULAR LOCATION SecretedCC -- TISSUE SPECIFICITY Expressed by the liver and secreted in plasmahelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

hellipDR GO GO0005615 Cextracellular space TASProtIncDR GO GO0015232 Fheme transporter activity TASProtIncDR GO GO0005506 Firon ion binding IEAUniProtKB-KWDR GO GO0006879 Pcellular iron ion homeostasis TASProtIncDR GO GO0015886 Pheme transport TASProtIncDR GO GO0044419 Pinterspecies interaction between organisms IEAUniProtKB-KWhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipSQ SEQUENCE 462 AA 51676 MW 054B44D0603763B8 CRC64 MARVLGAPVA LGLWSLCWSL AIATPLPPTS AHGNVAEGET KPDPDVTERC SDGWSFDATT

LDDNGTMLFF KGEFVWKSHK WDRELISERW KNFPSPVDAA FRQGHNSVFL IKGDKVWVYP PEKKEKGYPK LLQDEFPGIP SPLDAAVECH RGECQAEGVL FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC FQGNQFLRFD PVRGEVPPRY PRDVRDYFMP CPGRGHGHRN GTGHGNSTHH GPEYMRCSPH LVLSALTSDN HGATYAFSGT HYWRLDTSRD GWHSWPIAHQ WPQGPSAVDA AFSWEEKLYL VQGTQVYVFL TKGGYTLVSG YPKRLEKEVG TPHGIILDSV DAAFICPGSSRLHIMAGRRL WWLDLKSGAQ ATWTELPWPH EKVDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE KLNAAKALPQ PQNVTSLLGC TH

Extractable features

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 3: The Website was developed thanks to the

bull Itrsquos the study of the set of proteins expressed by a certain tissue or organism in a determined momentbull This discipline studies the proteome the set of proteins of an organism or a biological system (Mark Wilkins 1994)

techniques (separation and identification of proteins analysis of proteins sequence etchellip)

identification of a marker or a peptide markers pattern useful for the clinical diagnosis of a pathology

Many databases (IPI UniProtKB EMBL Nucleotide Sequence Database

Ensembl) contain information about proteins obtained directly by laboratory

experiments or by scientific literature

Web Services Choreography In order to organize understand and

better use of the knowledge

A Web Service as defined by W3C is a software system designed for the interoperability between different elaborators connected by the same network

Web services can be combined (choreography) in order to solve the problem of information integration between the databases in a functional and repeatable process

Web services standardize the mechanisms by which different machines can interact giving some services

They respond to HTTP requests formatted by SOAP syntax

SOAP (Simple Object Access Protocol) is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks and underlies the Web Services message protocol

This protocol is based on XML meta-language

WSDL is a document based on XML which contains a set of definitions that permits to specify web service features

ltwsdldefinitionsxmlnssoapenc=httpschemasxmlsoaporgsoapencoding xmlnsapachesoap=httpxmlapacheorgxml-soap xmlnstns1=httpexceptionsjdbfetchebiacuk xmlnswsdlsoap=httpschemasxmlsoaporgwsdlsoap xmlnsxsd=httpwwww3org2001XMLSchema xmlnsimpl=httpwwwebiacukwsservicesWSDbfetch xmlnsintf=httpwwwebiacukwsservicesWSDbfetch targetNamespace=httpwwwebiacukwsservicesWSDbfetch xmlnswsdl=httpschemasxmlsoaporgwsdlgt

ID HEMO_HUMAN Reviewed 462 AAAC P02790 B2R957DT 21-JUL-1986 integrated into UniProtKBSwiss-ProtDT 01-OCT-1996 sequence version 2DT 10-FEB-2009 entry version 99DE RecName Full=HemopexinDE AltName Full=Beta-1B-glycoproteinDE Flags PrecursorGN Name=HPXOS Homo sapiens (Human)OC Eukaryota Metazoa Chordata Craniata Vertebrata EuteleostomiOC Mammalia Eutheria Euarchontoglires Primates HaplorrhiniOC Catarrhini Hominidae HomoOX NCBI_TaxID=9606helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphellipCC -- FUNCTION Binds heme and transports it to the liver for breakdownCC and iron recovery after which the free hemopexin returns to theCC circulationCcCC -- SUBUNIT Interacts with HEV ORF3 proteinCC -- SUBCELLULAR LOCATION SecretedCC -- TISSUE SPECIFICITY Expressed by the liver and secreted in plasmahelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

hellipDR GO GO0005615 Cextracellular space TASProtIncDR GO GO0015232 Fheme transporter activity TASProtIncDR GO GO0005506 Firon ion binding IEAUniProtKB-KWDR GO GO0006879 Pcellular iron ion homeostasis TASProtIncDR GO GO0015886 Pheme transport TASProtIncDR GO GO0044419 Pinterspecies interaction between organisms IEAUniProtKB-KWhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipSQ SEQUENCE 462 AA 51676 MW 054B44D0603763B8 CRC64 MARVLGAPVA LGLWSLCWSL AIATPLPPTS AHGNVAEGET KPDPDVTERC SDGWSFDATT

LDDNGTMLFF KGEFVWKSHK WDRELISERW KNFPSPVDAA FRQGHNSVFL IKGDKVWVYP PEKKEKGYPK LLQDEFPGIP SPLDAAVECH RGECQAEGVL FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC FQGNQFLRFD PVRGEVPPRY PRDVRDYFMP CPGRGHGHRN GTGHGNSTHH GPEYMRCSPH LVLSALTSDN HGATYAFSGT HYWRLDTSRD GWHSWPIAHQ WPQGPSAVDA AFSWEEKLYL VQGTQVYVFL TKGGYTLVSG YPKRLEKEVG TPHGIILDSV DAAFICPGSSRLHIMAGRRL WWLDLKSGAQ ATWTELPWPH EKVDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE KLNAAKALPQ PQNVTSLLGC TH

Extractable features

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 4: The Website was developed thanks to the

Many databases (IPI UniProtKB EMBL Nucleotide Sequence Database

Ensembl) contain information about proteins obtained directly by laboratory

experiments or by scientific literature

Web Services Choreography In order to organize understand and

better use of the knowledge

A Web Service as defined by W3C is a software system designed for the interoperability between different elaborators connected by the same network

Web services can be combined (choreography) in order to solve the problem of information integration between the databases in a functional and repeatable process

Web services standardize the mechanisms by which different machines can interact giving some services

They respond to HTTP requests formatted by SOAP syntax

SOAP (Simple Object Access Protocol) is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks and underlies the Web Services message protocol

This protocol is based on XML meta-language

WSDL is a document based on XML which contains a set of definitions that permits to specify web service features

ltwsdldefinitionsxmlnssoapenc=httpschemasxmlsoaporgsoapencoding xmlnsapachesoap=httpxmlapacheorgxml-soap xmlnstns1=httpexceptionsjdbfetchebiacuk xmlnswsdlsoap=httpschemasxmlsoaporgwsdlsoap xmlnsxsd=httpwwww3org2001XMLSchema xmlnsimpl=httpwwwebiacukwsservicesWSDbfetch xmlnsintf=httpwwwebiacukwsservicesWSDbfetch targetNamespace=httpwwwebiacukwsservicesWSDbfetch xmlnswsdl=httpschemasxmlsoaporgwsdlgt

ID HEMO_HUMAN Reviewed 462 AAAC P02790 B2R957DT 21-JUL-1986 integrated into UniProtKBSwiss-ProtDT 01-OCT-1996 sequence version 2DT 10-FEB-2009 entry version 99DE RecName Full=HemopexinDE AltName Full=Beta-1B-glycoproteinDE Flags PrecursorGN Name=HPXOS Homo sapiens (Human)OC Eukaryota Metazoa Chordata Craniata Vertebrata EuteleostomiOC Mammalia Eutheria Euarchontoglires Primates HaplorrhiniOC Catarrhini Hominidae HomoOX NCBI_TaxID=9606helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphellipCC -- FUNCTION Binds heme and transports it to the liver for breakdownCC and iron recovery after which the free hemopexin returns to theCC circulationCcCC -- SUBUNIT Interacts with HEV ORF3 proteinCC -- SUBCELLULAR LOCATION SecretedCC -- TISSUE SPECIFICITY Expressed by the liver and secreted in plasmahelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

hellipDR GO GO0005615 Cextracellular space TASProtIncDR GO GO0015232 Fheme transporter activity TASProtIncDR GO GO0005506 Firon ion binding IEAUniProtKB-KWDR GO GO0006879 Pcellular iron ion homeostasis TASProtIncDR GO GO0015886 Pheme transport TASProtIncDR GO GO0044419 Pinterspecies interaction between organisms IEAUniProtKB-KWhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipSQ SEQUENCE 462 AA 51676 MW 054B44D0603763B8 CRC64 MARVLGAPVA LGLWSLCWSL AIATPLPPTS AHGNVAEGET KPDPDVTERC SDGWSFDATT

LDDNGTMLFF KGEFVWKSHK WDRELISERW KNFPSPVDAA FRQGHNSVFL IKGDKVWVYP PEKKEKGYPK LLQDEFPGIP SPLDAAVECH RGECQAEGVL FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC FQGNQFLRFD PVRGEVPPRY PRDVRDYFMP CPGRGHGHRN GTGHGNSTHH GPEYMRCSPH LVLSALTSDN HGATYAFSGT HYWRLDTSRD GWHSWPIAHQ WPQGPSAVDA AFSWEEKLYL VQGTQVYVFL TKGGYTLVSG YPKRLEKEVG TPHGIILDSV DAAFICPGSSRLHIMAGRRL WWLDLKSGAQ ATWTELPWPH EKVDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE KLNAAKALPQ PQNVTSLLGC TH

Extractable features

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 5: The Website was developed thanks to the

A Web Service as defined by W3C is a software system designed for the interoperability between different elaborators connected by the same network

Web services can be combined (choreography) in order to solve the problem of information integration between the databases in a functional and repeatable process

Web services standardize the mechanisms by which different machines can interact giving some services

They respond to HTTP requests formatted by SOAP syntax

SOAP (Simple Object Access Protocol) is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks and underlies the Web Services message protocol

This protocol is based on XML meta-language

WSDL is a document based on XML which contains a set of definitions that permits to specify web service features

ltwsdldefinitionsxmlnssoapenc=httpschemasxmlsoaporgsoapencoding xmlnsapachesoap=httpxmlapacheorgxml-soap xmlnstns1=httpexceptionsjdbfetchebiacuk xmlnswsdlsoap=httpschemasxmlsoaporgwsdlsoap xmlnsxsd=httpwwww3org2001XMLSchema xmlnsimpl=httpwwwebiacukwsservicesWSDbfetch xmlnsintf=httpwwwebiacukwsservicesWSDbfetch targetNamespace=httpwwwebiacukwsservicesWSDbfetch xmlnswsdl=httpschemasxmlsoaporgwsdlgt

ID HEMO_HUMAN Reviewed 462 AAAC P02790 B2R957DT 21-JUL-1986 integrated into UniProtKBSwiss-ProtDT 01-OCT-1996 sequence version 2DT 10-FEB-2009 entry version 99DE RecName Full=HemopexinDE AltName Full=Beta-1B-glycoproteinDE Flags PrecursorGN Name=HPXOS Homo sapiens (Human)OC Eukaryota Metazoa Chordata Craniata Vertebrata EuteleostomiOC Mammalia Eutheria Euarchontoglires Primates HaplorrhiniOC Catarrhini Hominidae HomoOX NCBI_TaxID=9606helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphellipCC -- FUNCTION Binds heme and transports it to the liver for breakdownCC and iron recovery after which the free hemopexin returns to theCC circulationCcCC -- SUBUNIT Interacts with HEV ORF3 proteinCC -- SUBCELLULAR LOCATION SecretedCC -- TISSUE SPECIFICITY Expressed by the liver and secreted in plasmahelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

hellipDR GO GO0005615 Cextracellular space TASProtIncDR GO GO0015232 Fheme transporter activity TASProtIncDR GO GO0005506 Firon ion binding IEAUniProtKB-KWDR GO GO0006879 Pcellular iron ion homeostasis TASProtIncDR GO GO0015886 Pheme transport TASProtIncDR GO GO0044419 Pinterspecies interaction between organisms IEAUniProtKB-KWhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipSQ SEQUENCE 462 AA 51676 MW 054B44D0603763B8 CRC64 MARVLGAPVA LGLWSLCWSL AIATPLPPTS AHGNVAEGET KPDPDVTERC SDGWSFDATT

LDDNGTMLFF KGEFVWKSHK WDRELISERW KNFPSPVDAA FRQGHNSVFL IKGDKVWVYP PEKKEKGYPK LLQDEFPGIP SPLDAAVECH RGECQAEGVL FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC FQGNQFLRFD PVRGEVPPRY PRDVRDYFMP CPGRGHGHRN GTGHGNSTHH GPEYMRCSPH LVLSALTSDN HGATYAFSGT HYWRLDTSRD GWHSWPIAHQ WPQGPSAVDA AFSWEEKLYL VQGTQVYVFL TKGGYTLVSG YPKRLEKEVG TPHGIILDSV DAAFICPGSSRLHIMAGRRL WWLDLKSGAQ ATWTELPWPH EKVDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE KLNAAKALPQ PQNVTSLLGC TH

Extractable features

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 6: The Website was developed thanks to the

They respond to HTTP requests formatted by SOAP syntax

SOAP (Simple Object Access Protocol) is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks and underlies the Web Services message protocol

This protocol is based on XML meta-language

WSDL is a document based on XML which contains a set of definitions that permits to specify web service features

ltwsdldefinitionsxmlnssoapenc=httpschemasxmlsoaporgsoapencoding xmlnsapachesoap=httpxmlapacheorgxml-soap xmlnstns1=httpexceptionsjdbfetchebiacuk xmlnswsdlsoap=httpschemasxmlsoaporgwsdlsoap xmlnsxsd=httpwwww3org2001XMLSchema xmlnsimpl=httpwwwebiacukwsservicesWSDbfetch xmlnsintf=httpwwwebiacukwsservicesWSDbfetch targetNamespace=httpwwwebiacukwsservicesWSDbfetch xmlnswsdl=httpschemasxmlsoaporgwsdlgt

ID HEMO_HUMAN Reviewed 462 AAAC P02790 B2R957DT 21-JUL-1986 integrated into UniProtKBSwiss-ProtDT 01-OCT-1996 sequence version 2DT 10-FEB-2009 entry version 99DE RecName Full=HemopexinDE AltName Full=Beta-1B-glycoproteinDE Flags PrecursorGN Name=HPXOS Homo sapiens (Human)OC Eukaryota Metazoa Chordata Craniata Vertebrata EuteleostomiOC Mammalia Eutheria Euarchontoglires Primates HaplorrhiniOC Catarrhini Hominidae HomoOX NCBI_TaxID=9606helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphellipCC -- FUNCTION Binds heme and transports it to the liver for breakdownCC and iron recovery after which the free hemopexin returns to theCC circulationCcCC -- SUBUNIT Interacts with HEV ORF3 proteinCC -- SUBCELLULAR LOCATION SecretedCC -- TISSUE SPECIFICITY Expressed by the liver and secreted in plasmahelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

hellipDR GO GO0005615 Cextracellular space TASProtIncDR GO GO0015232 Fheme transporter activity TASProtIncDR GO GO0005506 Firon ion binding IEAUniProtKB-KWDR GO GO0006879 Pcellular iron ion homeostasis TASProtIncDR GO GO0015886 Pheme transport TASProtIncDR GO GO0044419 Pinterspecies interaction between organisms IEAUniProtKB-KWhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipSQ SEQUENCE 462 AA 51676 MW 054B44D0603763B8 CRC64 MARVLGAPVA LGLWSLCWSL AIATPLPPTS AHGNVAEGET KPDPDVTERC SDGWSFDATT

LDDNGTMLFF KGEFVWKSHK WDRELISERW KNFPSPVDAA FRQGHNSVFL IKGDKVWVYP PEKKEKGYPK LLQDEFPGIP SPLDAAVECH RGECQAEGVL FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC FQGNQFLRFD PVRGEVPPRY PRDVRDYFMP CPGRGHGHRN GTGHGNSTHH GPEYMRCSPH LVLSALTSDN HGATYAFSGT HYWRLDTSRD GWHSWPIAHQ WPQGPSAVDA AFSWEEKLYL VQGTQVYVFL TKGGYTLVSG YPKRLEKEVG TPHGIILDSV DAAFICPGSSRLHIMAGRRL WWLDLKSGAQ ATWTELPWPH EKVDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE KLNAAKALPQ PQNVTSLLGC TH

Extractable features

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 7: The Website was developed thanks to the

WSDL is a document based on XML which contains a set of definitions that permits to specify web service features

ltwsdldefinitionsxmlnssoapenc=httpschemasxmlsoaporgsoapencoding xmlnsapachesoap=httpxmlapacheorgxml-soap xmlnstns1=httpexceptionsjdbfetchebiacuk xmlnswsdlsoap=httpschemasxmlsoaporgwsdlsoap xmlnsxsd=httpwwww3org2001XMLSchema xmlnsimpl=httpwwwebiacukwsservicesWSDbfetch xmlnsintf=httpwwwebiacukwsservicesWSDbfetch targetNamespace=httpwwwebiacukwsservicesWSDbfetch xmlnswsdl=httpschemasxmlsoaporgwsdlgt

ID HEMO_HUMAN Reviewed 462 AAAC P02790 B2R957DT 21-JUL-1986 integrated into UniProtKBSwiss-ProtDT 01-OCT-1996 sequence version 2DT 10-FEB-2009 entry version 99DE RecName Full=HemopexinDE AltName Full=Beta-1B-glycoproteinDE Flags PrecursorGN Name=HPXOS Homo sapiens (Human)OC Eukaryota Metazoa Chordata Craniata Vertebrata EuteleostomiOC Mammalia Eutheria Euarchontoglires Primates HaplorrhiniOC Catarrhini Hominidae HomoOX NCBI_TaxID=9606helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphellipCC -- FUNCTION Binds heme and transports it to the liver for breakdownCC and iron recovery after which the free hemopexin returns to theCC circulationCcCC -- SUBUNIT Interacts with HEV ORF3 proteinCC -- SUBCELLULAR LOCATION SecretedCC -- TISSUE SPECIFICITY Expressed by the liver and secreted in plasmahelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

hellipDR GO GO0005615 Cextracellular space TASProtIncDR GO GO0015232 Fheme transporter activity TASProtIncDR GO GO0005506 Firon ion binding IEAUniProtKB-KWDR GO GO0006879 Pcellular iron ion homeostasis TASProtIncDR GO GO0015886 Pheme transport TASProtIncDR GO GO0044419 Pinterspecies interaction between organisms IEAUniProtKB-KWhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipSQ SEQUENCE 462 AA 51676 MW 054B44D0603763B8 CRC64 MARVLGAPVA LGLWSLCWSL AIATPLPPTS AHGNVAEGET KPDPDVTERC SDGWSFDATT

LDDNGTMLFF KGEFVWKSHK WDRELISERW KNFPSPVDAA FRQGHNSVFL IKGDKVWVYP PEKKEKGYPK LLQDEFPGIP SPLDAAVECH RGECQAEGVL FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC FQGNQFLRFD PVRGEVPPRY PRDVRDYFMP CPGRGHGHRN GTGHGNSTHH GPEYMRCSPH LVLSALTSDN HGATYAFSGT HYWRLDTSRD GWHSWPIAHQ WPQGPSAVDA AFSWEEKLYL VQGTQVYVFL TKGGYTLVSG YPKRLEKEVG TPHGIILDSV DAAFICPGSSRLHIMAGRRL WWLDLKSGAQ ATWTELPWPH EKVDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE KLNAAKALPQ PQNVTSLLGC TH

Extractable features

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 8: The Website was developed thanks to the

ID HEMO_HUMAN Reviewed 462 AAAC P02790 B2R957DT 21-JUL-1986 integrated into UniProtKBSwiss-ProtDT 01-OCT-1996 sequence version 2DT 10-FEB-2009 entry version 99DE RecName Full=HemopexinDE AltName Full=Beta-1B-glycoproteinDE Flags PrecursorGN Name=HPXOS Homo sapiens (Human)OC Eukaryota Metazoa Chordata Craniata Vertebrata EuteleostomiOC Mammalia Eutheria Euarchontoglires Primates HaplorrhiniOC Catarrhini Hominidae HomoOX NCBI_TaxID=9606helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphellipCC -- FUNCTION Binds heme and transports it to the liver for breakdownCC and iron recovery after which the free hemopexin returns to theCC circulationCcCC -- SUBUNIT Interacts with HEV ORF3 proteinCC -- SUBCELLULAR LOCATION SecretedCC -- TISSUE SPECIFICITY Expressed by the liver and secreted in plasmahelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

hellipDR GO GO0005615 Cextracellular space TASProtIncDR GO GO0015232 Fheme transporter activity TASProtIncDR GO GO0005506 Firon ion binding IEAUniProtKB-KWDR GO GO0006879 Pcellular iron ion homeostasis TASProtIncDR GO GO0015886 Pheme transport TASProtIncDR GO GO0044419 Pinterspecies interaction between organisms IEAUniProtKB-KWhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip

helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipSQ SEQUENCE 462 AA 51676 MW 054B44D0603763B8 CRC64 MARVLGAPVA LGLWSLCWSL AIATPLPPTS AHGNVAEGET KPDPDVTERC SDGWSFDATT

LDDNGTMLFF KGEFVWKSHK WDRELISERW KNFPSPVDAA FRQGHNSVFL IKGDKVWVYP PEKKEKGYPK LLQDEFPGIP SPLDAAVECH RGECQAEGVL FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC FQGNQFLRFD PVRGEVPPRY PRDVRDYFMP CPGRGHGHRN GTGHGNSTHH GPEYMRCSPH LVLSALTSDN HGATYAFSGT HYWRLDTSRD GWHSWPIAHQ WPQGPSAVDA AFSWEEKLYL VQGTQVYVFL TKGGYTLVSG YPKRLEKEVG TPHGIILDSV DAAFICPGSSRLHIMAGRRL WWLDLKSGAQ ATWTELPWPH EKVDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE KLNAAKALPQ PQNVTSLLGC TH

Extractable features

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 9: The Website was developed thanks to the

The website can be visited only by authorized users through an authentication with username and password

From the Home Page we can reach the other pages of Protmine website

rsaquo Load file PF2Drsaquo Show file PF2Drsaquo Compare scorersaquo Load Proteins Listrsaquo Show Proteins Listrsaquo Search Proteinrsaquo Search GOrsaquo Prediction Algorithmrsaquo Contacts

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 10: The Website was developed thanks to the

In order to facilitate the localization of proteins into the uploaded files we have built the following pagesrsaquo Search Proteinrsaquo Search GO

In order to know if a protein has a transmembrane helix we have added this pagersaquo Prediction Algorithm

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 11: The Website was developed thanks to the

Between the informations searched fromthe website there are those related to

Gene Ontology GO0005829 Ccytosol TASProtInc

Gene Symbol HGNC TPM2 Transmembrane TRANSMEM 17 37 Signal-

anchor for type II membrane Glycosylation CARBOHYD 184 184 N-linked

(GlcNAc)

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 12: The Website was developed thanks to the

There are 3 types of secondary structure of proteins

rsaquo α-helix (alpha helix)rsaquo β-sheet (beta structure) rsaquo turns

We can talk about topology if we consider

The domains crossing the membrane () are usually but not

necessary alpha-helixes

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 13: The Website was developed thanks to the

We studied several algorithms for prediction of protein secondary structure including

Chou-Fasman based on a calculation of the propensity of each of the 20 amino acids to be found in each of the three secondary structures considered

Sosua use amphipathicity and hydrophobicityparameters of each of the 20 amino acids

TMHMM they apply a probabilistic approach such as Hidden Markov Model

Gromiha based on a conformational switch on the occurrences of amino acid residues in the transmembrane helix of the membrane protein (FM) and frequency of occurrence throughout the complex (FT)

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 14: The Website was developed thanks to the

Protein primary structure

Shape parameter

fm = occurrences of amino acid residues in the transmembrane helixft = occurrences of amino acid residues in the protein complex

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 15: The Website was developed thanks to the

a Replacing of each element of the amino acid sequence with 1 or 0 depending on the α parameter value (ie if it is respectively greater or less than 080)

b Segmentation of the amino acid sequence in subparts that contain at least 18 points in a row with an index of high priority (1) and at least three consecutive zeros inside

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 16: The Website was developed thanks to the

c Segments analysis using mobile windows of four amino acids to ensure that in these subdivisions there are not two zeros

d If the previous condition is verified you stop the segment after the last 1 and select the longer segment as transmembrane helix

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 17: The Website was developed thanks to the

Division of the segments that contain more than 40 amino acids so that the child segments containing at least 18 elements with the least number of zeros

Retranslation of the numbers sequences into amino acid to view the monomers that make up the transmembrane helix

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 18: The Website was developed thanks to the

Using other databases to increase the information available

Graphic display of certain information

Correlate the obtained protein profiles with diagnosis possibly standardized

  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22
Page 19: The Website was developed thanks to the
  • Diapositiva numero 1
  • ProtMine New (1)
  • ProtMine New (2)
  • ProteomicS (1)
  • ProteomicS (2)
  • Web ServiceS (1)
  • Web ServiceS (2)
  • Web Services Description Language
  • Extracted data File
  • Protmine Sections
  • SEARCH and PREDICTION
  • Additional Information into the website
  • Additional Information into the website
  • Secondary structure topology
  • Prediction algorithms
  • Gromiha Algorithm
  • Gromiha Algorithm STEPS (1)
  • Gromiha Algorithm STEPS (2)
  • Gromiha Algorithm Final STEPS
  • Gromiha Algorithm Final STEPS
  • Conclusions and future development
  • Diapositiva numero 22

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