[Bioperl-l] generate a fasta file from the blast report

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Mon Apr 30 20:22:35 EDT 2007


> if i have the following script working on my blast report, can anyone plz
> tell me how can i generate a fasta format file of just the hits (subject)
> sequence.

Do you want the WHOLE subject sequence, or just the region that hit the query?

The hit is available as $hsp->hit_string();
http://doc.bioperl.org/bioperl-live/Bio/Search/HSP/GenericHSP.html#CODE11

The whole subject sequence would require the original Fasta input file.

By the way, are your questions for work related issues, or is this
your homework or assignment for a study course?

--Torsten


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