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Banche dati specializzate. Banche dati Specializzate. Le banche dati specializzate raccolgono insiemi di dati omogenei dal punto di vista tassonomico e/o funzionale disponibili nelle Banche dati Primarie e/o in Letteratura, rivisti e annotati con informazioni di valore aggiunto.

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banche dati specializzate1

Banche dati Specializzate

Le banche dati specializzate raccolgono insiemi di dati omogenei dal punto di vista tassonomico e/o funzionale disponibili nelle Banche dati Primarie e/o in Letteratura, rivisti e annotati con informazioni di valore aggiunto

banche dati specializzate di patterns proteici

Banche dati Specializzate di Patterns Proteici

  • Data una sequenza non caratterizzata:
    • A che famiglia appartiene?
    • Qual è la sua funzione?
the protein signature approach
“The protein signature approach”
  • Confrontiamo sequenze appartenenti alla stessa famiglia, cercando ‘pattern’ comuni
  • Costruiamo un database di profili conservati (elementi di sequenza conservati in specifiche posizioni)
  • Usiamo questi profili (pattern) per classificare una sequenza incognita
slide5
Multiple sequence alignment

What are protein signatures?

Protein family/domain

Build model

Search

UniProt

Protein analysis

Significant match

ITWKGPVCGLDGKTYRNECALL

Mature model

AVPRSPVCGSDDVTYANECELK

slide6
Diagnostic approaches (sequence-based)

Single motif methods

Regex patterns (PROSITE)

Full domain alignment methods

Profiles

(Profile Library)

HMMs

(Pfam)

Multiple motif methods

Identity matrices

(PRINTS)

slide7
Motif

Define pattern

xxxxxx

xxxxxx

xxxxxx

xxxxxx

Extract pattern sequences

Build regular expression

C-C-{P}-x(2)-C-[STDNEKPI]-x(3)-[LIVMFS]-x(3)-C

Pattern signature

PS00000

Patterns

Sequence alignment

protein families
Protein families
  • PFAM (acronimo di Protein Families) è un database di domini di proteine descritti con modelli markoviani. E’ diviso in due sezioni: pfam-A contiene allineamenti curati da esperti; pfam-B contiene sequenze che vengono automaticamente raggruppate.
slide14
InterPro Entry

Groups similar signatures together

Adds extensive annotation

Adds extensive annotation

Links to other databases

Links to other databases

Structural information and viewers

  • Hierarchical classification
interpro hierarchies families
Interpro hierarchies: Families

FAMILIES can have parent/child relationships with other Families

  • Parent/Child relationships are based on:
  • Comparison of protein hits
  • child should be a subset of parent
  • siblings should not have matches in common
  • Existing hierarchies in member databases
  • Biological knowledge of curators
interpro hierarchies domains
Interpro hierarchies: Domains

DOMAINS can have parent/child relationships with other domains

slide18
InterPro Entry

Groups similar signatures together

Adds extensive annotation

Adds extensive annotation

Links to other databases

Links to other databases

Structural information and viewers

slide19
InterPro Entry

Groups similar signatures together

Adds extensive annotation

Adds extensive annotation

Links to other databases

Links to other databases

Structural information and viewers

The Gene Ontology project provides a controlled vocabulary of terms for describing gene product characteristics

slide20
InterPro Entry

Groups similar signatures together

Adds extensive annotation

Adds extensive annotation

Links to other databases

Links to other databases

Structural information and viewers

UniProt

KEGG ... Reactome ... IntAct ...

UniProt taxonomy

PANDIT ... MEROPS ... Pfam clans ...

Pubmed

slide21
InterPro Entry

Groups similar signatures together

Adds extensive annotation

Adds extensive annotation

Links to other databases

Links to other databases

Structural information and viewers

PDB 3-D Structures

SCOP Structural domains

CATH Structural domain classification

searching interpro1
Searching InterPro

Protein family membership

Domain organisation

Domains, repeats

& sites

GO terms

banche dati specializzate associate a patterns nucleotidici

Banche dati Specializzateassociate a Patterns Nucleotidici

Eukaryotic Promoter Database (http://www.epd.isb-sib.ch/)

Transcription Factors TRANSFAC

Translation Terminations TransTERM

Vector database VectorDB

Repeats Database Repbase

profili strutturali

Profili strutturali

CATH (http://www.cathdb.info/)

SCOP (http://scop.mrc-lmb.cam.ac.uk/scop/)

banche dati specializzate di
Banche dati Specializzate di
  • Geni
  • Genomi
  • Trascritti e Profili di Espressione
  • Pathways Metabolici
  • Mutazioni
banche dati specializzate di geni
Banche dati Specializzatedi Geni
  • COGs
  • Entrez Gene
  • RefSeq
siti genomici

Siti Genomici

NCBI Genomes

EBI Genomes

TIGR (Craig Venter)

il genoma umano

Il Genoma Umano

Il Genoma Umano all’NCBI

Il Genoma Umano alla Celera

Ensembl

UCSC Genome Bioinformatics

banche dati del trascrittoma

Banche dati del Trascrittoma

dbEST

UniGene

UTRdb/UTRsite

banche dati di espressione

Banche dati di Espressione

GEO

ArrayExpress

EPDex

banche dati di pathways metabolici

Banche dati diPathways Metabolici

Kyoto Encyclopedia

of Genes and Genomes

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

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