identification of gene from databases

8/14/2019 Identification of Gene From Databases

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Identification of

Genes fromDatabasesPresented to

Dr.C.G. JoshiProfessor

Department of Animal Biotechnology,College of Veterinary Science & A.H.,Anand

Presented byPatel Hiren M

MVsc(Anim .Biotechnology)


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Introduction

Evolution is somewhat conservative

Evolution seems to have often involved the

duplication and divergence of gene Certain sequence may indicate a certain

function

A structural set of data held in a computer The structures of new genes are constantly

adding


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Databases

Require Some Basic Knowledge

What is gene

What is gene structure

- Prokaryotes

- Eukaryotes

ORFs (Open Reading Frame) cDNA library

Human genome project


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Prokaryote Genome

In prokaryotes ,introns are less common and

genes often contain a single uninterrupted

stretch of DNA, called a cistron, that codes

for a product.

These functionally related genes are in

clustered and can be transcribed together on

same mRNA


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Eukaryotic Genes

Much more complex than in prokaryotes.

Large genomes (0.1 to 3 billion bases)

A typical mammalian cell has 1,500 times asmuch DNA than the cell ofE. Coli.

Low coding density (


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Gene Structure Eukaryotes


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Data Mining

Development of new tools for datamining

Sequence alignment

Genome sequencing

Genome comparison

Micro array data analysis

Proteomics data analysis

Small molecular array analysis


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What is a database?

A database is a collection ofinformation stored in a computer in a

systematic way, such that acomputer program can consult it toanswer questions

The software used to manage andquery a database is known as adatabase management system(DBMS)

The properties of database systems


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Annotation Forms

PubMed

Select articles that are notcited on RegulonDB

Read and select abstracts withtranscriptional information

REGULONDB

Enter data into databasethrough annotation forms

Read complete articlesabout conditions

Read completegeneral articles

Articledatabase

Selected

abstracts

Is this a general

article?

Keywords

Search

Found

Articles

Articles Classification


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Annotation formsRegistration Format


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Annotation forms


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What makes a gooddatabase?

Quality

Manual (slow)

No overlapbetween entries

Reliable

Some datamight be missing

Coverage

Automatic (fast)

Overlappingentries

Errors, biases

Up-to-date


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for Gene

Identification Find candidate genes for the trait

(time and cost!)

-What genes are there?

-How gene are expressed

-What do they do?

-How could they play a role inthe disease

-Gene synonyms

-Gene location


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GENE SCORING


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DATA SOURCES

PubMed Conserved Domain Database

Conserved Domain Database

GeneAtlas

dbSNP

Links to above-mentioned databases:Gene: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genePubMed: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMedCDD: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cddHomologene:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologeneGeneAtlas: http://wombat.gnf.org/


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Gene Databases

Once a genome is in place, it isdesirable to study the regions thatmake a particular organism what it

is.

One such resource is located in thegenetic regions of the organism,

Several databases of genes andrelated structures exist.

Such database is the RefSeq

database curated at NCBI.


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Classification of Databases

Primary sequence databases

Secondary sequence databases

Genomic database resource


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Secondary sequence databases

Unigene:-Historical use for selecting sequences for micro

array. The TIGR Gene Indices:-

The gene indices at the institute for geneticresearch are arranged according to species.The TIGR GI covers 19 animal species, 18 plant

species and 7 fungal species. TIGR also include fullinformation about splice variance in the database.

Ref Seq. (NCBI References Sequence Project):-The Ref Seq. aims to collect sequences of

genomes, complete chromosome genomic regions;mRNAs & other type of RNA.


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What are genomedatabases?

Genome databases contain, well,genomic information collected frommany sources.

Genome assembly Gene predictions

Known genes, mRNA, ESTs, proteins

Genetic maps, markers andpolymorphisms

Gene expression and phenotypes

Annotations

Interspecies homologues


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Genomic Database Resource

Ensembl

- http://www.ensembl.org

19 species

UCSC Genome Browser- http://genome.ucsc.edu/

28 species (Insects!)

NCBI MapViewer- http://www.ncbi.nlm.nih.gov/mapview/

38 species (Plants, Fungi!)


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Queries to Ensembl


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Browsegenome

Quicksearch


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Quick search results


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Geneviewlink


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Gene View


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Various Gene Databases

are: SNP Resources

- dbSNP: database of single nucleotide

polymorphismshttp://www.ncbi.nlm.nih.gov/

SNP/

- SNP Consortiumdatabase:http://snp.cshl.org/

rSNP

Guide:http://util.bionet/nsc.ru/database


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SNPs at NCBI


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Select SNPdatabase

Free text query goes

tohere


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Accession numberfor the

SNP, and species.

Location of the SNP inthesequence

Links toalternative

views


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Various Gene Databasesare:

EST Resources

- ESTs are expressed sequence tags,which are partial copies of mRNAfound within a particular cell.

- Information from ESTs can be usedto tell the splicing patterns of

genes,he occurrence of genes, etc.

dbESThttp://www.ncbi.nlm.nih.gov/dbEST/


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Protein Databases

-The process of the central dogma statesthat DNA gets coded into RNA, which inturn gets turned into proteins.

- Since proteins code for genes, it isimportant to store known information aboutproteins inside of databases.

- There are many different proteindatabases, many of them dealing withspecific protein families.

Databases for curated proteins include:

InterPro: Protein families and domainshtt ://www.ebi.ac.uk/inter ro


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Protein Sequence Motifs(Domains)

- CDD:

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

- eMOTIF:

http://motif.stanford.edu/emotif/- Pfam:http://www.sanger.ac.uk/Software/Pfa

Structure Databases

-
http://www.sanger.ac.uk/Software/Pfam/http://www.sanger.ac.uk/Software/Pfam/


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Gene Expression Databases- Once the location and sequence of

genes is known, the next step is todetermine their function.- Various biological experiments can be

performed on gene data, including thenewer microarray technology which wewill cover in class

- Databases containing the results ofthis experimental data are available

KEGG http://www.genome.ad.jp/kegg/

Klotho http://www.ibc.wustl.edu/klotho


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Comparison of Sequence

against Sequence Database The most commonly used programmes for

comparing an unknown sequence against

the sequence the database are BLAST,

FASTA.

BLAST and FASTA are derivatives of

Smith - Watermann Algorithm.


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The FASTA algorithm

Developed by Lipman and Pearson 1985

First program to search sequence

databases for gapped local alignment The best scoring local region is given as

output

It is an approximate heuristic algorithmused to compute sub-optimal pair wisesimilarity.

http://www-nbrf.georgetown.edu/pirwww/s

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http://www-nbrf.georgetown.edu/pirwww/search/fasta.htmlhttp://www-nbrf.georgetown.edu/pirwww/search/fasta.html


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BLAST

BLASTn

Megablast

Nucleotide querry BLASTx Protein querry tBLASTn,

Nucleotide querry tBLASTx

Conserved Domains RPS-BLAST,CDART

Pairwise BLAST 2BLAST

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What is BLAST?

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BLAST (Basic LocalAlignment Search Tool) is aset of similarity search programs designed to

explore all of the available sequence databases

regardless of whether the query is protein or

DNA.

local means it searches and aligns sequence

segments, rather than align the entire sequence.

Its able to detect relationships among sequenceswhich share only isolated regions of similarity.

Currently, it is the most popular and most

accepted sequence analysis tool.

Wh BLAST?


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Why BLAST?

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Identify unknown sequences - The best way to

identify an unknown sequence is to see if thatsequence already exists in a public database. If

the database sequence is a well-characterized

sequence, then you may have access to a wealth

of biological information.

Help gene/protein function and structure

prediction genes with similar sequences tend to

share similar functions or structure.

Identify protein family group related (paralog or

ortholog) genes and their proteins into a family.

Prepare sequences for multiple alignments


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Go to BLAST


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Go tonucleotide

BLAST


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Bl t 1


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Blast 1

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Blast 2


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Blast 2

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Blast limit by


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Blast limit bytaxon

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Bl t lt


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Blast results

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Interpret BLAST results


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Interpret BLAST results -Distribution

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This image shows the distribution of BLAST hits on the query sequence. Each

line represents a hit. The span of a line represents the region where similarity is

detected. Different colors represent different ranges of scores.

Query sequence

BLAST hits. Click

to access the

pairwise

alignment.

Interpret BLAST results


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Interpret BLAST results -Description

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ID (GI #, refseq #, DB-specific

ID #) Click to access therecord in GenBank

Bit score higher, better.Click to access the

pairwise alignment

Expect value lower, better. It

tells the possibility that this isa random hit

Gene/sequence

Definition

The description (also called definition) lines are listed below under the

heading "Sequences producing significant alignments". The term"significant" simply refers to all those hits whose E value was less than the

threshold. It does not imply biological significance.

Link

s

I t t BLAST lt


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Interpret BLAST results pairwise alingments

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Query line: the segment from query sequence.

Subj line: the segment from hit (subject) sequence.

Middle line: the consensus bases

SOFTWARES FOR


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SOFTWARES FOR

IDENTIFICATION OF GENES

Some computational tools that are most

commonly used for gene prediction

Gene MarkGlimmer M

GRAIL

GenScanGenebuilder

G M k


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Gene Mark

This software was developed by MarkBorodovsky and James Mc Ininch.

This is used for finding prokaryotic

genes. This software employs non-homogenous markov model toclassify DNA regions into protein

coding, non-coding sequences


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Glimmer

This software was developed bySteven Salzberg et al. at JohnsHopkins University and TIGR.

Glimmer uses interpolated markovmodels to identify coding regionsand distinguish them from non-

coding DNA. Glimmer is used as theprimary gene finder tool at TIGR.


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GRAIL

This software was developed by EdUberbacher et al. at Oakridgenational laboratory. This tool

identifies exons, polyA sites,promoters, CpG islands, repetitiveelements and frame shift errors in

DNA sequences by comparing themto a database of known Human andMouse sequence elements.


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GenScan

GenScan was developed by ChrisBurge and Samuel Karlin atStanford University. Thisprogramme uses probabilistic

model of gene structure that isbased on actual biologicalinformation about thetranscriptional, translational and

splicing signals. Its high speed andaccuracy make GenScan themethod of choice for the initialanalysis of large stretches of

eukaryotic genomic DNA. GenScan


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Genebuilder

Genebuilder performs ab initio geneprediction using numerousparameters, such as GC content, di-

codon frequencies, splicing sitedata, CpG islands, repetitiveelements and others. It also

performs BLAST searches ofpredicted genes against protein andEST databases.

Sequence analysis: overview


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q y

Nucleotide sequence file

Search databases for

similar sequences

Sequence comparison

Multiple sequence analysis

Design further experimentsRestriction mappingPCR planning

Translate

into protein

Search for

known motifs

RNA structure

prediction

non-coding

coding

Protein sequence

analysis

Search for protein

coding regions

Manual

sequence entry

Sequence database

browsing

Sequencing project

management

Protein sequence file

Search databases forsimilar sequences

Sequence comparison

Search forknown motifs

Predictsecondary

structure

Predict

tertiary

structureCreate a multiple

sequence alignment

Edit the alignment

Format the alignment

for publication

Molecular

phylogeny

Protein family

analysis

Nucleotide

sequence

analysis

Sequence

entry


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identification of gene from databases

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