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Curr Protoc Bioinformatics. 2002 Aug;Chapter 3:Unit 3.2. doi: 10.1002/0471250953.bi0302s00.

Finding homologs to nucleic acid or protein sequences using the framesearch program.

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


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.

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