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

Mike Marchywka marchywka at hotmail.com
Tue Jul 29 03:08:04 EDT 2008

> 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."  

Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
415-264-8477 (w)<- use this
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only
marchywka at hotmail.com
Note: If I am asking for free stuff, I normally use for hobby/non-profit
information but may use in investment forums, public and private.
Please indicate any concerns if applicable.
Note: Hotmail is possibly blocking my mom's entire
ISP - try  me on marchywka at yahoo.com if no reply
here. Thanks.

Time for vacation? WIN what you need- enter now!

More information about the BBB mailing list