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

[Lambert, Lisa]

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