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Biological Databases
Pharmamatrix 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, SWISSMODEL 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
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Sequences
Accession number
References
Taxonomic data
Annotation/curation
Keywords
Cross-references
Documentation
NCBI
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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 NCBI
Example: PubMed, taxonomy, SNP, PubChem
etc.
Tools for analysis
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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
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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
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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