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J Virol Methods. 2008 Sep;152(1-2):98-101. doi: 10.1016/j.jviromet.2008.06.009. Epub 2008 Jul 17.

SWeBLAST: a Sliding Window Web-based BLAST tool for recombinant analysis.

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1
Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.

Abstract

We describe a simple Perl computer tool for matching successive subsequences of a query sequence using the BLAST facilities of Genbank. SWeBLAST helps identify 'parents' of recombinant sequences, even when these are themselves unrelated, thus it is complementary to methods that compare sets of aligned homologous sequences, and avoids the significant problem of these methods in having first to decide which sequences to compare. SWeBLAST searches may also be valuable for checking the recombination history of genes proposed for use as transgenes.

PMID:
18602951
DOI:
10.1016/j.jviromet.2008.06.009
[Indexed for MEDLINE]
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