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

D W Collins1

  • 1Space Sciences Laboratory, Oakland, CA 94608.

Computer Applications in the Biosciences : CABIOS
|June 1, 1993
PubMed
Summary

Fast Index Search for Homologous coding sequences (FISH) is a database and software tool for efficiently searching protein-coding gene sequences. It allows rapid identification of similar sequences using numerical descriptions, bypassing the need for functional annotation or alignments.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Efficiently searching and organizing large genetic sequence databases is crucial for biological research.
  • Existing methods may require extensive computational resources or detailed sequence alignments.

Purpose of the Study:

  • To introduce Fast Index Search for Homologous coding sequences (FISH), a novel database and software package.
  • To provide a tool for rapid directory of protein-coding gene sequences.

Main Methods:

  • FISH utilizes a database containing numerical descriptions of 22,361 DNA sequences from GenBank release 69.0.
  • Numerical representations include nucleotide counts, synonymous codon counts, and GenBank LOCUS names.
  • The software allows querying by LOCUS name, sequence length, or DNA sequence comparison using distance measures.

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Main Results:

  • The FISH index provides a comprehensive directory of protein-coding gene sequences.
  • The software enables rapid assembly of lists of similar coding sequences.
  • Search times are typically under a minute on standard microcomputers.

Conclusions:

  • FISH offers a fast and efficient method for searching homologous coding sequences.
  • The tool facilitates discovery of similar sequences without functional annotation or sequence alignments.
  • FISH is a valuable resource for bioinformatics and genomics research.