[Biodevelopers] request for help on bioinformatics problem

[danag]

on 9/09/02 11:03 AM, bioinfo at bioinfo at biosystemsconsulting.com wrote:

> Andrew,
> How long are the read windows that you are looking for?  You
> might be able to use blast without the gaping functions and set a window
> size to the length of homologous bases your looking for.  Just a
> thought.
> 
> Mark
> 
> -----Original Message-----
> From: biodevelopers-admin at bioinformatics.org
> [mailto:biodevelopers-admin at bioinformatics.org] On Behalf Of Andrew
> Bagshaw
> Sent: Saturday, September 07, 2002 1:28 AM
> To: biodevelopers at bioinformatics.org
> Subject: [Biodevelopers] request for help on bioinformatics problem
> 
> 
> Hello,
> 
> I am trying to find homologous pairs from among thousands of 50 bp
> sequences as part of my bioinformatics research. Could someone please
> advise if there is any software available anywhere that will do this
> job?
> 
> Andrew Bagshaw
> Doctoral student in genetics
> University of Canterbury
> New Zealand
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> 
May be you should use Multiple ungapped alignment such as Blocks analysis.
http://blocks.fhcrc.org/
-- 
Dana Reichmann