Lisa I believe the vmatch tool (a suffix array algorithm) has inputs that will handle that. I have used it for searching for pri-miRNAs where I wanted things in particular range of lengths. I can't remember the exact URL to get it, but a Google search will turn it up.
Regards Mike On Jul 28, 2008, at 2:36 PM, Lambert, Lisa wrote: > While comparing the promoters of a set of genes with similar > metabolic functions, I came across a region of around 270 bp that > was present in nine of the genes. I found this same region in the > same spot in the higher primates, but in no other species. The > lowest percent identity between genes is 69% and the highest is 86%. > I wanted to see if this region was associated with other genes, but > then I ran into a problem. When I try to do BLAT or BLASTN genomic > searches, I get a lot of "noise," especially with short, exact hits. > Changing the parameters at ENTREZ typically yields either a handful > of hits, or well over 150,000. ENSEMBL will return hits of 10 bp > with 100% identity while missing 250 bp with 75% identity. 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? > > Lisa Lambert > Chatham University > Pittsburgh, PA > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
