Hi Andrew, I'm cross-posting your question to the Sequence Search Mailing List (SSML). This should be a good place for a discussion of your problem. https://bioinformatics.org/mailman/listinfo/ssml-general Are you looking for only 5-7bp matches with no extension? How big is your oligo? One parameter that would need adjustment is E which should probably be set outrageously high (1e-10?). Can you share the seq3.fasta sequence? I could try blasting against refseq too or against some sequence that you know it should hit. Regards, Joey ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Joseph A Bedell, Ph.D. Director, Bioinformatics Orion Genomics, LLC 4041 Forest Park Ave. St. Louis, MO 63108 Office:(314)615-6979; Fax:(314)615-6975 Mobile:(314)518-1343 http://www.oriongenomics.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >-----Original Message----- >From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l- >bounces at portal.open-bio.org] On Behalf Of Andrew Walsh >Sent: Wednesday, March 03, 2004 1:52 PM >To: bioperl-l at portal.open-bio.org >Subject: [Bioperl-l] Small word sizes with BLAST (WU, NCBI) > >Hello, > >My question is not really related to a specific Bioperl library, so I >apologize. If there is a specific 'BLAST' newsgroup, I will be happy to >post there. But I was hoping somebody on the Bioperl list had some >experience doing nucleic acid searches with small word sizes. > >I would like to search for small (5-7) bp matches between an oligo >sequence >and a ~100,000 mRNA database. I've tried doing this with WU-BLAST and >NCBI-BLAST. NCBI-BLAST does not allow word sizes below 7, so I've tried >lots of different command line parameters for WU-BLAST. > >I've tried these searches with versions 2.0a19 (alpha) and 2.0 of WU-BLAST. > >I get quite strange results when I start lowering the word size below the >default (11). For example, with the alpha version, I get more hits with a >word size of 10 than I do with a word size of 7. With the beta version, I >get the same number of hits with word sizes 10 and 7. I've checked this by >hand, and the 'missing' hits do in fact have stretches of 7 continuous bps >matching. > >Here is an example of one of the command lines I've tried running: >blastn human_refseq.fasta seq3.fasta W=5 S=5 M=1 V=100000 B=100000 > >I've tried adjusting every parameter I thought would affect the search >results, but still cannot recover the 'missing' hits. > >Maybe BLAST is the wrong tool for this. I'd just like something that's >fast. If anyone has some advice, it would be greatly appreciated. > >Thanks a lot, > >Andrew > >_________________________________________________________________ >Add photos to your messages with MSN 8. Get 2 months FREE*. >http://join.msn.com/?page=dept/features&pgmarket=en- >ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgma rket >%3den-ca > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l