Thanks, Mike I've used PERL (I'll definitely take a look at BIOPERL), and could write something that locally searches downloaded FASTA results or whole genome files. I was just hoping I had missed something faster, since this is more of a side project than my main area of interest. It might be a good student project for the fall!
It also occurred to me (after sleeping on it) that, given the size, these might be SINEs, so I'm going to check Repeatmaster and see if I can narrow things that way. Lisa ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mike Marchywka [EMAIL PROTECTED] Sent: Tuesday, July 29, 2008 3:08 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Looking for a DNA search engine that includes length as a parameter > 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 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
