DBT - Department of Biotechnology, India

International Nucleotide Sequence Database Collaboration

  • NCBI - National Center for Biotechnology Information (GenBank database and other stuff)
  • EBI - European Bioinformatics Institute (EMBL database and other stuff)
  • DDBJ - DNA Data Bank of Japan
  • Feature Table Definition - the format of entries in these databases

Protein Sequence Databases

  • SWISS-PROT & TrEMBL - annotated protein sequence database and computer annotated supplement
  • PIR - Protein Information Resource
  • MIPS - Munich Information centre for Protein Sequences

Database Searching by Sequence Similarity

Sequence Alignment

  • USC Sequence Alignment Server - align 2 sequences with all possible varieties of dynamic programming
  • T-COFFEE - multiple sequence alignment
  • ClustalW @ EBI - multiple sequence alignment
  • DiAlign - multiple sequence alignment
  • POA - partial order alignment
  • BOXSHADE - pretty printing and shading of multiple alignments
  • Spidey - an mRNA-to-genomic alignment program
  • SIM4 - a program to align cDNA and genomic DNA
  • Wise2 - align a protein or profile HMM against genomic sequence to predict a gene structure, and related tools
  • PipMaker - computes alignments of similar regions in two (long) DNA sequences
  • VISTA - align + detect conserved regions in long genomic sequences
  • myGodzilla - align a sequence to its ortholog in the human genome
  • BAliBASE - a benchmark alignments database for the evaluation of multiple sequence alignment programs
  • Whole Genome Human/Mouse Alignments

Eukaryotic Genome Browsers

Genome Databases

Transcript Databases

  • Mammalian Gene Collection - full-length (open reading frame) sequences for human and mouse
  • FANTOM - Functional Annotation of Mouse cDNAs
  • STACK - Sequence Tag Alignment and Consensus Knowledgebase

Genome-Scale Analysis

  • MBGD - comparative analysis of completely sequenced microbial genomes
  • COGs - phylogenetic classification of orthologous proteins from complete genomes
  • STRING - detect whether a given query gene occurs repeatedly with certain other genes in potential operons
  • Pedant - automatic whole genome annotation
  • GeneCensus - various whole genome comparisons

Protein Domain Families and Motifs

  • InterPro - integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL
  • PROSITE - database of protein families and domains
  • Pfam - alignments and hidden Markov models covering many common protein domains
  • SMART - analysis of domains in proteins
  • ProDom - protein domain database
  • PRINTS Database - groups of conserved motifs used to characterise protein families
  • Blocks - multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins
  • Protein Domain Profile Analysis @ BMERC - search a library of profiles with a protein sequence
  • TIGRFAMs - yet more protein families based on Hidden Markov Models
  • ELM - the eukaryotic linear motif resource
  • ScanSite - search for phosphorylation & interaction sites in proteins

Motif and Pattern Finding in Sequences

  • Gibbs Motif Sampler - identification of conserved motifs in DNA or protein sequences
  • AlignACE Homepage - gene regulatory motif finding
  • MEME - motif discovery and search in protein and DNA sequences
  • SAM - tools for creating and using Hidden Markov Models
  • Pictogram - visualize base frequencies in DNA motifs

Protein 3D Structure Resources

Transmembrane Helix Prediction

RNA Folding

Phylogeny & Taxonomy

  • The Tree of Life
  • Species 2000 - index of the world's known species
  • TreeBASE - a database of phylogenetic knowledge
  • PHYLIP - package of programs for inferring phylogenies
  • MOLPHY - molecular phylogenetics
  • PAML - phylogenetic analysis by maximum likelihood
  • PAUP - tools for inferring and interpreting phylogenetic trees
  • TreeView - user friendly tree displaying

Gene Prediction

Comparative Gene Prediction

Gene Expression Databases

Gene Regulation Resources

Biomolecular Interaction & Network Databases

Miscellaneous Databases

Miscellaneous Tools

Computational Resources

Web Sites for Background Information & News

Journals

Other Collections of Bioinformatics Resources