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Nucleotide Databases
· Protein Databases · Sequence Similarity Searching · Sequence Alignment · Genome Browsers
· Genome Databases · Transcript Databases · Genome-scale Analysis · Protein Domains & Motifs · Motif Finding · Protein 3D Structure
· Transmembrane Helices · RNA Folding · Phylogeny & Taxonomy · Gene Prediction · Comparative Gene Prediction · Gene Expression
· Gene Regulation · Biomolecular Networks · Miscellaneous Databases · Miscellaneous Tools · Computational Resources · Information · Journals ·
Other Lists
- 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
- SWISS-PROT
& TrEMBL - annotated protein sequence database and computer annotated
supplement
- PIR - Protein Information
Resource
- MIPS - Munich Information
centre for Protein Sequences
- 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
- 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
- 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
- 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
- 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
- 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
Please send suggestions to: Jie Wang
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