Bioperl: Help with blast and vector trimming

[Rubin Eitan]

I have a less than perfect code for masking (i.e. replacing a region in a 
sequence with Ns). It's 15 minutes for a seasoned perl programmer *i.e. 2 
hours for me), but it may be helpful. Bioperl invites etc.

       Eitan.  


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Eitan Rubin,
Plant Genetics, Weizmann Inst of Science, Rehovot, Israel.  
EMail: bcrubin@dapsas1.weizmann.ac.il
Tel: (00972)-(8)9342421 Fax: (00972)-(8)9344181
EitanR@BioMOO (http://bioinfo.weizmann.ac.il/BioMOO) - visit 
                                            the GCG help desk

in vivo -> in vitro -> in silico
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On Fri, 29 Jan 1999, Jonathan Epstein wrote:

> I'm trying to use the bioPerl blast functionality, initially for trimming
> vector from some EST's.
> 
> When I run the sample:
> perl ./blast_seq.pl seq/seqs.fasta -eid -prog blastp -db yeast -signif
> 1e-5 -table 2 >runseqs.out
> I encounter the following error, even though the named file exists.
> 
> UX:sh (sh): ERROR:
> /disk3/people/epstein/perl/lib/site_perl/Bio/Tools/Blast/Run/postclient.pl:
> Not found
> No Blast results saved.
> 
> 
> As long as I have your attention, trimming vector sequence looks to be
> pretty simple using these utilities, but if anyone has a little bit of code
> to contribute, I would be grateful.
> 
> Regards,
> 
> - Jonathan
> 
> 
> 
> Jonathan Epstein                                Jonathan_Epstein@nih.gov
> Unit on Biologic Computation                    (301)402-4563
> Office of the Scientific Director               Bldg 31, Room 2A31
> Nat. Institute of Child Health and Development  31 Center Drive
> National Institutes of Health                   Bethesda, MD 20892
> 
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