[Bioperl-l] Parsing Blast Report

Scott Markel SMarkel at accelrys.com
Wed Mar 25 15:20:12 EDT 2009


No.  The full-length hit sequences are not in the BLAST report.
You need to use either NCBI's fastacmd (in same set of executables
that has formatdb and blastall) or some database look-up.


Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
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> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> Sent: Wednesday, 25 March 2009 12:05 PM
> To: bioperl-l
> Subject: [Bioperl-l] Parsing Blast Report
> Hi All,
>         Is there any way i can get the hit sequence from the blast report?
> I am using SearchIO module to parse the blast report.
> Thanks
> Shalabh
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