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Bioinformatics Resources on the Web

Major Data Submission Centers

NCBI (National Center for Biotechnology Information)
EBI (European Bioinformatics Institute)
RCBI/PDB (Research Collaboratory for Structural Bioinformatics)

Archival or Primary Databases

GenBank at NCBI
UNIPROT at EBI (previously SWISS-PROT and TrEMBL)
PDB (Protein Data Bank) at RCSB -Structural Database

Derived or Value-added Databases

Sequence Databases

PROSITE (A database of protein profiles and patterns)
PRODOM (ThePROteinDOMain Database-built from UNIPROT)
PFAM (Protein families database of alignments and HMMs)
BLOCKS (Blocks WWW Server obtained from PROSITE)
INTERPRO (Integrated Resource of Protein Domains and Functional Sites)
Integr8 (Integrated browser to access complete genomes and proteomes at EBI)

Structure Databases

CATH (Class Architecture, Topology & Homologous super family)
SCOP (Structural Classification of Proteins)
FSSP (Fold classification based on Structure-Structure alignment of Proteins)
HSSP (A database of Homology-derived Secondary Structure of Proteins | MSAs for PDBs)
HOMSTRAD (Homologous Structure Alignment Database)
DSSP (Database of Secondary Structure Assignments)
VAST (Vector Alignment Search Tool)

Specialized Databases/Web Resources

UCSC Genome Browser
GO (The Gene Ontology)
KEGG (Kyoto Encyclopedia of Genes and Genomes)
OMIM (Online Mendelian Inheritance in Man)
ENZYME (Enzyme Nomenclature Database)
BRENDA (Comprehensive Enzyme Database)
PMD (Protein Mutant Database)
COG (Clusters of Orthologous Groups of proteins)
DIP (Database of Interacting proteins)

Useful Tools

BLAST (Pair-wise sequence alignment tools)
CLUSTALW (Multiple sequence alignment tool)
CD-HIT (Protein sequence clustering tool)
PROFILEMAKE (Builds profiles for sequence families)
HMMER (Software suite for sequence analysis using HMMs)
PHYLIP (Software suite for phylogenetic analysis)
PIPMAKER (Software suite for sequence comparison)
MVIEW (Multiple sequence alignment viewer)
JALVIEW (Multiple sequence alignment viewer and editor)

Data Formats

Interesting Bioinformatics Resources

Bioinformatics Education

Suggested Reading

Tutorial on Blast Statistics