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Genbank : GenBank® is a sequence database that contains publicly available DNA sequences for more than 170,000 different organisms. GenBank data is accessible through NCBI?s retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.
UniGene UniGene provides an organized view of transcribed sequences by collapsing them into groups that correspond to genes and then connecting these entries to other classes of information that may shed light on gene expression and function. Tools provided on the UniGene web site allow researchers to browse cDNA libraries by developmental stage or tissue of origin, view surrogate expression profiles based on EST counts, and find groups of genes with similar expression patterns.

COG :The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on phylogenetic classification of the proteins encoded in complete genomes. Each COGs includes proteins that are inferred to be orthologs (direct evolutionary counterparts). The current release consists of 138,458 which form 4873 COGs and comprise 75% of the 185,505 proteins from 50 bacterial genomes, 13 archaeal genomes, and three genomes of unicellular eukaryotes. The COG database is updated periodically as new genomes become available.

EMBL The EMBL Nucleotide Sequence Database (URL : http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. Network services allow free access to the most up-to-date data collection. For sequence similarity searching a variety of tools (e.g. Fasta, BLAST) are available.

Ensembl : Ensembl is a joint project between EMBL-EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes. This site provides free access to all the data and software from the Ensembl project.

TIGR Gene Indices : Analysis of the public EST sequences, available through the TIGR Gene Indices (TGI ; http://www.tigr.org/tdb/tdb.html), is an attempt to identify the genes represented by that data and to provide functional, structural, and evolutionary information regarding those genes. Gene Indices are constructed by first clustering, then assembling EST and annotated gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or Tentative Consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, and to provide links between orthologous and paralogous genes.

ASDB - Alternative Splicing Database : ASDB consists of two divisions, ASDB (proteins), which contains amino acid sequences, and ASDB (nucleotides) with genomic sequences. The protein entries from SwissProt are joined into clusters corresponding to alternatively spliced variants of one gene. The DNA division consists of complete genes with alternative splicing mentioned or annotated in GenBank. The search engine allows one to search over SwissProt and GenBank fields and then follow the links to all variants.

Last update on 5 June 2008