> From: [EMAIL PROTECTED] > To: [email protected] > 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] if no reply here. Thanks. > _________________________________________________________________ Time for vacation? WIN what you need- enter now! http://www.gowindowslive.com/summergiveaway/?ocid=tag_jlyhm _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
