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FISH: a guide to protein-coding DNA sequences in the GenBank database.

D W Collins
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Abstract

FISH (Fast Index Search for Homologous coding sequences) consists of a database and associated software and is intended to function as a directory of protein-coding gene sequences. The FISH index contains descriptions of 22,361 DNA sequences from release 69.0 of the GenBank genetic sequence database. Complete coding sequences are represented numerically with counts of nucleotides and synonymous codons, and with GenBank LOCUS names and short descriptions. The software permits the database to be queried by GenBank LOCUS name, sequence length (expressed as total number of codons), or by comparison with a DNA sequence. In the latter case, the numerical descriptions are compared with simple distance measures in place of actual DNA sequences. The FISH package can be used to rapidly assemble lists of similar coding sequences, without regard to functional annotation or sequence alignments. Typical search times are well under a minute on widely available IBM-compatible microcomputers.

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AlgorithmsAmino Acid SequenceBase SequenceDatabase Management SystemsGene LibraryMolecular Sequence DataSoftwareUser-Computer InterfaceJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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D W Collins. 1993. FISH: a guide to protein-coding DNA sequences in the GenBank database.. https://doi.org/10.1093/bioinformatics%2F9.3.337

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