[BiO BB] Looking for a DNA search engine that includes length as a parameter

[Mike Marchywka]

> From: Lambert at Chatham.edu
> To: bbb at bioinformatics.org
> Date: Mon, 28 Jul 2008 15:36:35 -0400
> Subject: [BiO BB] Looking for a DNA search engine that includes length as a parameter
>

>[...]What I really is an engine where I can specify that only hits longer than 200 bp with an identity of at least 50% be returned. Does anyone know of a tool that will do this?

In the past, I've written scripts to download search results non-selectively and then 
sort through them locally with custom criteria. I'm a programmer so this is my approach to everything but I think it makes sense whenever you expect to do a lot of ad hoc or exploratory processing.
One of the well know packages, I think people keep mentioning bioperl, may be worth considering
rather than hoping to find a specific search engine that does exactly what you want.
 
In my case, I was looking for 25bp long DNA sequences and wanted to find "what is close by"
in various species. IIRC, the things I hoped to find "close by" were sequences close to different 
25bp probes in my query list. So, I did blast searches on genomes and then extracted the hit locations,
requested expanded versions of the approriate chromosomes, and fiddled with the results
using text processing scripts. 

I guess effectively I had a query that looked like, " find areas that contain 10, 25bp sequences in
any order, with matches being better than 20/25 for each key sequence, and  not more than about 300bp in total span."  



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