Help with searching an oligonucleotide database

Peter Rice pmr at sanger.ac.uk
Fri Jun 11 03:05:44 EST 1999


aiyar at ebv.oncology.wisc.edu (Ashok Aiyar) writes:
> I have a large number of oligonucleotide sequences available as
> as fasta format database.  These oligos range in length from 15
> nucleotides to about 100 nucleotides.  
> 
> I would like to search a larger sequence (3 - 5 kb) against this 
> database -- so that I can identify all the oligos that lie in the 
> large sequence, and use them as PCR primers or whatever.
> 
> What publically available programs are suitable for this search? 

There will are applications in EMBOSS that we can easily modify to do
this.  Sounds like a good idea - we will add it soon.

EMBOSS is the European Molecular Biology Open Software Suite
of sequence analysis programs. It is GPL (and LGPL) licensed and
is currently available as a pre-beta release.

The EMBOSS home page is http://www.sanger.ac.uk/Software/EMBOSS/

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/




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