Biological DatabasesPharmamatrix Workshop 2010

- Philip Winter - Ishwar V. Hosamani

Some databases in the field of molecular biology…

AATDB, AceDb, ACUTS, ADB, AFDB, AGIS, AMSdb, ARR, AsDb,BBDB, BCGD,Beanref,Biolmage,

BioMagResBank, BIOMDB, BLOCKS, BovGBASE,BOVMAP, BSORF, BTKbase, CANSITE, CarbBank,CARBHYD, CATH, CAZY, CCDC, CD4OLbase, CGAP,

ChickGBASE, Colibri, COPE, CottonDB, CSNDB, CUTG,CyanoBase, dbCFC, dbEST, dbSTS, DDBJ, DGP, DictyDb,Picty_cDB, DIP, DOGS, DOMO, DPD, DPlnteract, ECDC,ECGC, EC02DBASE, EcoCyc, EcoGene, EMBL, EMD db,ENZYME, EPD, EpoDB, ESTHER, FlyBase, FlyView,GCRDB, GDB, GENATLAS, Genbank, GeneCards,

Genline, GenLink, GENOTK, GenProtEC, GIFTS,GPCRDB, GRAP, GRBase, gRNAsdb, GRR, GSDB,

HAEMB, HAMSTERS, HEART-2DPAGE, HEXAdb, HGMD,HIDB, HIDC, HlVdb, HotMolecBase, HOVERGEN, HPDB,HSC-2DPAGE, ICN, ICTVDB, IL2RGbase, IMGT, Kabat,

KDNA, KEGG, Klotho, LGIC, MAD, MaizeDb, MDB,Medline, Mendel, MEROPS, MGDB, MGI, MHCPEP5

Micado, MitoDat, MITOMAP, MJDB, MmtDB, Mol-R-Us,MPDB, MRR, MutBase, MycDB, NDB, NRSub, 0-lycBase,OMIA, OMIM, OPD, ORDB, OWL, PAHdb, PatBase, PDB,PDD, Pfam, PhosphoBase, PigBASE, PIR, PKR, PMD,

PPDB, PRESAGE, PRINTS, ProDom, Prolysis, PROSITE,PROTOMAP, RatMAP, RDP, REBASE, RGP, SBASE,

SCOP, SeqAnaiRef, SGD, SGP, SheepMap, Soybase,SPAD, SRNA db, SRPDB, STACK, StyGene,Sub2D,

SubtiList, SWISS-2DPAGE, SWISS-3DIMAGE, SWISS-MODEL Repository, SWISS-PROT, TelDB, TGN, tmRDB,TOPS, TRANSFAC, TRR, UniGene, URNADB, V BASE,VDRR, VectorDB, WDCM, WIT, WormPep, YEPD, YPD,

YPM, etc .................. !!!!

What we expect from a database..!!

• Sequence, functional, structural information, related bibliography

• Well Structured and Indexed• Well cross-referenced (with other databases)• Periodically updated• Tools for analysis and visualization

Biological Databases

• Sequence databases• Structure databases

Sequence databases

• Nucleotide databases• Protein databases

Sequence databases

Nucleotide databases

• International Nucleotide Sequence Database Collaboration (INSDC)– NCBI– EMBL– DDBJ

Standard contents of a sequence database

• Sequences• Accession number• References• Taxonomic data• Annotation/curation• Keywords• Cross-references• Documentation

NCBI

• Very comprehensive biological database• GENBANK: The nucleotide sequence database• Provides 42 different resource• Provides a simple and easy to use web

interface

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

• Sequence submission: done using Bankit or Sequin

• Search Engine for data retrieval: Entrez• Retrieves information across all the resources

under NCBIExample: PubMed, taxonomy, SNP, PubChem etc.

Tools for analysis

• BLAST• Primer-BLAST• B-Link• ORF finder• Genome workbench

Protein Sequence databases

• UniProt• PFAM• Gene Index project

UniProt

• Universal Protein Resource• Formed through the merger of :– SIB– EBI-SwissProt– TrEMBL– PIR-PSD

• Entry names are often the names of the gene followed by the species.

• Accession numbers are of the following format:

• e.g. P26367 (PAX6_HUMAN)

Uniprot features

• Blast• Align• Retrieve• ID mapping

Pfam

• Proteins contain conserved regions• Based on the conserved regions, proteins are

classified into families• Provides links to external databases like PDB,

SCOP, CATH etc.

Pfam: Features

• Sequence search• View Pfam family• View a clan• View a sequence• View a structure• Keyword search

Gene Indices• Project aimed at indexing genes and their

variants in the various genome sequences.

• Creating a catalogue of genes in a wide range of organisms

• Reduce redundancy

Gene Indices Software Tools

• TGI Clustering tools• Clview• SeqClean• Cdbfasta/cdbyank

Structural databases

• PDB – Protein Data Bank• CATH• SCOP – Structural Classification of Proteins

wwPDB

• Contains information about experimentally determined structures of proteins, nucleic acids, and complex assemblies

• RCSB-PDB, PDBe, PDBj, BMRB – repositories of protein structure data

• Files in PDB, mmCIF, PDBML/XML formats

• Advanced search – provides comprehensive information about a protein.

• Sequence info, domain info, sequence similarity, literature, apart from the details of the structure.

• Cross referenced to SCOP and CATH

CATH

• Classification of proteins based on domain structures

• Each protein chopped into individual domains and assigned into homologous superfamilies.

• Hierarchial domain classification of PDB entries.

CATH hierarchy

• Class – derived from secondary structure content is assigned automatically• Architecture – describes gross orientation of secondary

structures, independent of connectivity• Topology – clusters structures according to their

topological connections and numbers of secondary structures• Homologous superfamily – this level groups

together protein domains which are thought to share a common ancestor and can therefore be described as homologous

SCOP

• Description of structural and evolutionary relationships between all the proteins with known structures

• Uses the PDB entries• Search using keywords or PDB identifiers

Hierarchy in SCOP

• Class• Fold• Superfamily• Family

• Species

Thank you