Unit

UNIT 3.2 Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program

  1. Matthew Healy

Published Online: 1 AUG 2002

DOI: 10.1002/0471250953.bi0302s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Healy, M. 2002. Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program. Current Protocols in Bioinformatics. 00:3.2:3.2.1–3.2.23.

Author Information

  1. Bristol-Myers Squibb Pharmaceutical Research Institute, Wallingford, Connecticut

Publication History

  1. Published Online: 1 AUG 2002
  2. Published Print: JAN 2003

Abstract

The Framesearch algorithm includes the possibility of a frameshift error in its alignment algorithm, and therefore can find alignments that span different reading frames. Protocols in this unit describe the use of Framesearch to search a protein sequence database for sequences that are similar to a query nucleotide sequence, and to search a nucleotide sequence database for sequences that are similar to a query protein sequence. Three alternate protocols describe ways to improve the speed of Framesearch and thus make it practical for routine use. Framesearch is especially appropriate for low-quality single-read nucleotide sequence data, such as ESTs (expressed sequence tags) or early drafts of genomic sequences; it does not offer any significant advantage over less CPU-intensive algorithms for relatively high-quality nucleotide sequences without many single-nucleotide insertion or deletion errors.