SWeBLAST

SWeBLAST identifies recombinant sequences by matching successive subsequences of a query sequence to sequences in GenBank using BLAST, enabling detection of parental sequences without prior alignment or a predefined comparison set.

Key Features:

• Implementation: Implemented in Perl and using BLAST facilities to query GenBank sequences.
• Non-aligned Sequence Analysis: Operates on non-aligned query sequences by matching successive subsequences rather than requiring an initial multiple sequence alignment.
• Identification of Unrelated Parent Sequences: Detects potential parent sequences involved in recombination even when those parents are not closely related.
• Complementary Methodology: Provides an alternative approach to methods that rely on aligned homologous sequences by not requiring a predefined set of comparison sequences.
• Recombination History Verification: Supports verification of the recombination history of genes proposed for use as transgenes.

Scientific Applications:

• Genetic Research: Aids analysis of evolutionary dynamics by identifying recombinant sequences and their putative origins.
• Transgenic Studies: Assesses recombination history of candidate genes proposed for transgenesis to check for unintended recombinant elements.
• Virology and Pathogen Evolution: Traces recombinant events in viral genomes and pathogens to study genetic diversity and adaptation.

Methodology:

Implemented in Perl, SWeBLAST performs successive subsequence BLAST queries of a query sequence against sequences in GenBank using BLAST facilities, enabling identification of potential parent sequences without prior alignment or selection of comparison sequences.