bioinformatika - university of belgradepoincare.matf.bg.ac.rs/~nina/bioinf/1/cas01.pdfuvod -...
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BIOINFORMATIKA
Čas 1
1. Uvod
2. Osnovni pojmovi molekularne biologije
3. Korišćenje bioinformatičkih baza podataka
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UVOD – PROGRAM KURSA
Uvod u molekularnu biologiju i bioinformatiku
Algoritmi uprarivanja niski, sufiksna stabla
Poravnanje sekvenci – lokalno, globalno,
višestruko
Matrice supstitucije; heurističke metode
pretraživanja baza podataka
Filogenetsko stablo
Probabilistički modeli sekvenci: MM, HMM i
primene u bioinformatici
Istraživanje podataka i teksta u bioinformatici
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UVOD - LITERATURA
Computational Molecular Biology – An
Introduction – P.Clote, R.Backofen
Bioinformatics – Mathematical and
Computational Methods – A.Polansky, M.Kimmel
Biological Sequence Analysis –Probabilistic
Models of Proteins and Nucleic Acids – R.Durbin,
S.Eddy, A.Krogh, G.Mitchinson
Algoritmic Aspects of Bioinformatics –
H.J.Böckenhauer ,D.Bongartz
Introduction to Mathematical Methods in
Bioinformatics – A.Isaev
Exploring bioinformatics - a practical based
approach – C. St. Clair,J. Visick
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UVOD - POLAGANJE
Ispit
Projekat
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UVOD – BIOLOŠKI PODACI
Organizam
DNK, RNK – sastavljene od nukleotida –
niska nad azbukom A,C,G,T
proteini – sastavljeni od aminokiselina –
niska nad 20toslovnom azbukom
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UVOD – BIOLOŠKI PODACI
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UVOD
Bioinformatika se bavi dizajnom, konstrukcijom i
korišćenjem softverskih alata za generisanje,
čuvanje, obeležavanje, pristup i analizu bioloških
informacija
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UVOD
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OSNOVNI POJMOVI MOLEKULARNE BIOLOGIJE
Genom
Hromozom
DNK –Gen
Kodon, antikodon
RNK
Ekson, intron
Splicing
Protein
Struktura – primarna, sekundarna
Homolozi, ortolozi, izoformi
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Ćelija
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Ćelija – prokariote i eukariote
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Ćelija – makromolekuli
Makromolekuli koji učestvuju u funkcionisanju
svake ćelije su:
1. DNK
2. RNK
3. proteini
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DNK Dezoksiribonukleinska kiselina
sadrži instrukcije potrebne za
razvoj i funkcionisanje svakog
organizma
dva lanca koji su sastavljeni od
nukleotida – trokomponentnih
organskih jedinjenja od kojih su
za funkciju DNK najvažnije
azotne baze A,C,G,T
međusobno se povezuju preko
azotnih baza i to uvek A-C, G-T
redosled azotnih baza <=>
genetska instrukcija
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DNK
DNK se nalazi u ćeliji, organizovana u strukture
koje se nazivaju hromozomi
Ljudski hromozom 13 sadrži dnk molekul dužine
oko 2.3cm
Unutar hromozoma, DNK molekul je gusto
sabijen
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DNK - SAVIJANJE
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DNK
Prokariote – hromozomi se nalaze u citoplazmi;
pored hromozoma, u prokariotama i nekim
eukariotama DNK može formirati i druge
strukture, npr plazmidi
Eukariote – hromozomi se nalaze u jedru; pored
jedra, DNK se nalazi i u nekim organelama kao
što su mitohondrije i hloroplasti
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RNK
Ribonukleinska kiselina
učestvuje u različitim
ćelijskim procesima
mRNK, rRNK, tRNK
razlika u odnosu na DNK:
hemijski sastav (riboza -
dezoksiriboza) i azotna
baza U umesto T
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Geni, genom
Gen - deo DNK koji sadrži informaciju potrebnu
za sintezu jednog proteina ili jednog molekula
RNK
Genom – skup svih gena koje sadrži jedna ćelija
organizma
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Sinteza proteina
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Sinteza proteina
http://www.youtube.com/watch?v=NJxobgkPEAo
&feature=related
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Genetski kod
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Protein
niska nad 20toslovnom azbukom
Primarna struktura – niz aa
Sekundarna struktura – uređenost delova proteina u helikse ili ravni
Tercijarna struktura – 3d oblik celog proteina
http://upload.wikimedia.org/wikipedia/commons/c/c9/Main_protein_structure_levels_en.svg
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PROTEINI - AMINOKISELINE
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Protein
Homolozi – proteini koji potiču od istog pretka;
mogu biti iz različitih vrsta (ortolozi) ili iz iste
vrste (paralozi)
Izoformi – različiti oblici istog proteina
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PROTEIN - PRIMERI
Protein Uloga
Alfa-keratin Izgradnja kose
Beta-keratin Izgradnja krljušti
Insulin Regulacija nivoa šećera u krvi
Aktin, miosin Kontrakcija mišića
DNK polimeraza Sinteza DNK
Hemoglobin Transport kiseonika
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KORIŠĆENJE BIOINFORMATIČKIH BAZA
PODATAKA
NCBI – Nacionalni centar za biotehnološke
informacije, SAD
EBI – Evropski bioinformatički institut, UK
SBI – Švajcarski bioinformatički institut
KEGG – Kjotovska enciklopedija gena i genoma
…
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NCBI
Nacionalni centar za biotehnološke informacije
izgradnja javnih baza podataka
istraživanja u računarskoj biologiji
razvoj softverskih alata za analizu sekvenci
http://www.ncbi.nlm.nih.gov
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NCBI – baze podataka
primarne: GenBank, Trace, SRA, SNP, GEO
sekundarne: NCBI Protein, Refseq, TPA,
RefSNP, GEO datasets, UniGene, Homologene,
Structure, Conserved Domain
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NCBI - GenBank
baza genetskih sekvenci
GenBank projekat je deo International
Nucleotide Sequence, Database Collaboration:
DNA DataBank of Japan (DDBJ), the European
Molecular Biology Laboratory (EMBL) i NCBI
primer: swine flu
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NCBI - Entrez
sistem za pretraživanje više baza podataka
pretraga po ključnoj reči cancer
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NCBI - BLAST
Basic Local Alignment Search Tool
lokalno poravnanje date sekvence sa izabranom bazom ili dve date sekvence
heuristički pristup zasnovan na Smit-Votermenovom algoritmu
najkorišćeniji bioinformatički alat
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KEGG
Kyoto Encyclopedia of Genes and Genomes
računarska reprezentacija biološkog sistema
kolekcija baza podataka koje obuhvataju oblasti
genoma, enzimatskih puteva i bioloških
jedinjenja
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KEGG
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KEGG
kolekcija ručno iscrtanih grafičkih dijagrama,
takozvanih KEGG mapa puteva, koji
predstavljaju prikaz različitih hemijskih reakcija
kod metaboličkih procesa, obrade genetskih
informacija, obrade informacija koje dolaze iz
spoljašnje sredine, bolesti čoveka...
primer: Type II diabetes mellitus
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EBI
Evropski bioinformatički institut
deo Evropske laboratorije za molekularnu
biologiju (EMBL)
najveća kolekcija različitih baza podataka i alata
za rad sa njima
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EBI
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EBI - Ensembl
centralna baza podataka različitih genoma -
humanog i drugih
zajednički projekat EBI i Wellcome Trust Sanger
Instituta
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SBI
Švajcarski bioinformatički institut
razvoj baza podataka i softverskih alata
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SBI - ExPaSy
Expert Protein Analysis System
prvi server za potrebe molekularne biologije
analiza proteinskih sekvenci i njihovih struktura
http://www.expasy.org
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SBI - UniProt
Swiss Institute of Bioinformatics – UniProt
Universal Protein Resource
centralna baza podataka o proteinima
zajednički projekat SBI, EBI i PIR (Protein
Information Resource)
http://www.uniprot.org
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SBI – UniProt
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SBI – UniProtKB/SwissProt
sve trenutno poznate informacije o odre.enom
proteinu (o funkciji proteina, strukturi,
modikacijama,...)
ručna anotacija - proveravanje karakteristika
koje su automatski dodeljene proteinu
http://www.uniprot.org/uniprot/P00740
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ZADATAK
NCBI vežba