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

Michael Muratet mmuratet at hudsonalpha.com
Mon Jul 28 16:23:35 EDT 2008


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.



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
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