[Bioperl-l] OK for aa seq but not a na seq on RemoteBlast.pm version 1.28

Chris Fields cjfields at uiuc.edu
Thu Feb 16 16:37:25 EST 2006


As an update for those interested, I check on this today, feeding SearchIO
XML and text output for all NCBI's BLAST flavors.  Basically, all XML parses
fine.  All text output except blastn and tblastx works fine.  The last two
have the extra lines starting with 'Features in this part of subject
sequence:'.  I'll be checking into SearchIO::blast but don't know when I can
get around to posting a fix.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Pieter Monsieurs
> Sent: Thursday, February 16, 2006 3:46 AM
> To: gyang at plantbio.uga.edu
> Cc: bioperl-l at lists.open-bio.org; Chris Fields
> Subject: Re: [Bioperl-l] OK for aa seq but not a na seq on RemoteBlast.pm
> version 1.28
> 
> Hi,
> 
> I have the same problem with the blast.pm-file.
> The people of NCBI added some extra info when giving the Blast-output.
> (see e.g. "Features flanking this part..." or "Features in this part
> ..."), example added.
> The blast.pm module starts looking for the hsp-alignement-information,
> but it dies when it hits this Feature-information.
> 
> Pieter
> 
> 
......







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