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Identification of protein coding regions by database similarity search

Nature Genetics volume 3, pages 266–272 (1993)Cite this article

Abstract

Sequence similarity between a translated nucleotide sequence and a known biological protein can provide strong evidence for the presence of a homologous coding region, even between distantly related genes. The computer program BLASTX performed conceptual translation of a nucleotide query sequence followed by a protein database search in one programmatic step. We characterized the sensitivity of BLASTX recognition to the presence of substitution, insertion and deletion errors in the query sequence and to sequence divergence. Reading frames were reliably identified in the presence of 1% query errors, a rate that is typical for primary sequence data. BLASTX is appropriate for use in moderate and large scale sequencing projects at the earliest opportunity, when the data are most prone to containing errors.

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Author notes

  1. David J. States

    Present address: Institute for Biomedical Computing, Washington University, 700 S. Euclid Avenue, St. Louis, Missouri, 63110, USA

Authors and Affiliations

  1. National Center for Biotechnology Information, National Library of Medicine, Building 38A, Room 8N806, 8600 Rockville Pike, Bethesda, Maryland, 20894-0001, USA

    Warren Gish & David J. States

Authors
  1. Warren Gish
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  2. David J. States
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Gish, W., States, D. Identification of protein coding regions by database similarity search. Nat Genet 3, 266–272 (1993). https://doi.org/10.1038/ng0393-266

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