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

Mathieu Fourment¹, Adrian J Gibbs, Mark J Gibbs

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

Journal of Virological Methods

|July 8, 2008

Summary

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We developed SWeBLAST, a Perl tool for identifying recombinant sequence parents by matching successive subsequences. This method complements existing sequence comparison techniques and aids in analyzing gene recombination histories.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Identifying the origins of recombinant DNA sequences is crucial for understanding genetic diversity and evolution.
Existing methods for analyzing homologous sequences often require pre-selection of related sequences, which can be challenging for unrelated or complex recombinations.

Purpose of the Study:

To introduce SWeBLAST, a novel computational tool designed to identify 'parental' sequences of recombinant DNA.
To offer a complementary approach to existing sequence analysis methods, particularly for unrelated or complex recombinant sequences.
To facilitate the assessment of recombination history for genes intended for use as transgenes.

Main Methods:

Development of a Perl-based computer tool named SWeBLAST.

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Utilizing the Basic Local Alignment Search Tool (BLAST) facilities of GenBank for sequence matching.

Implementing a method for matching successive subsequences within a query sequence.

Main Results:

SWeBLAST effectively identifies 'parents' of recombinant sequences, even when these parents are not homologous.
The tool circumvents the need to pre-select sequences for comparison, a limitation of other methods.
Demonstrated utility in analyzing the recombination history of potential transgenes.

Conclusions:

SWeBLAST provides a valuable and complementary tool for analyzing recombinant sequences.
The method is particularly useful for identifying parents of sequences that may not be easily aligned using traditional homologous sequence comparison.
SWeBLAST can aid in evaluating the suitability of genes for transgene applications by examining their recombination history.