[Bioperl-l] use blast to extract similar sequences
Ross KK Leung
ross at cuhk.edu.hk
Fri Sep 16 04:51:38 EDT 2011
I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/- 20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!
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