[Bioperl-l] StandAloneBlastPlus blastdbcmd question

Anna Friedlander anna.fr at gmail.com
Mon Dec 19 07:09:15 UTC 2011


Hi all

I have a question about using blastdbcmd via
Bio::Tools::Run::StandAloneBlastPlus

I have some Blast+ search results that I am manipulating in a perl
programme, and I would like to retrieve some sequence information for
some results using subject sequence IDs, and associated subject start
and end indices. If I was using blastdbcmd directly, I would do so
using the -entry and -range options.

My question is, can I use all the blastdbcmd options (or more
specifically, just the -entry and -range options) from within the
StandAloneBlastPlus module?

My apologies if I don't properly understand how this "wrapper" works!

Thanks in advance for your help
Anna Friedlander



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