[Bioperl-l] SearchIO, StandAloneBlastPlus

Chris Fields cjfields at illinois.edu
Wed Mar 17 12:12:42 EDT 2010


How would you go about doing that from the BLAST report alone (which doesn't store the whole sequence)?  Unless you know something I don't, you'll need to pull the unique identifier for the sequence from the hit object while parsgin the report and grab the seq from a local or remote database (or use fastacmd or it's equivalent in blast+).


On Mar 15, 2010, at 3:15 AM, Janine Arloth wrote:

> Hello,
> exists a possibility to get/extract the whole hit sequences? (Not only the hit string from the alignment with $hsp->$hit_string;)
> Best regards
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