[BiO BB] HMMER on genomes
mgollery at unr.edu
Mon Jul 28 12:42:04 EDT 2003
Try GeneWise- you can download it at
But I will warn you- it is quite slow!
Quoting Peri Suraj <bioinfo_india at yahoo.com>:
> Hi Group,
> Did any one tried to build HMMs (using HMMER) for any
> gene class and then search genomes over this HMM.
> Although this is more perfect for proteins, how one
> can cope the problem of introns when you search
> genomic DNA where you build and train HMM on mRNAs
> (Exons). Can it be done. Unfortunately the makers of
> HMMER are politely denying to respond to such specific
> questions. Can any one please help.
> Suraj Peri
> Ph.D. Student
> School of Medicine
> Johns Hopkins University
> 600 North Wolfe Street
> Baltimore, MD 21287
> E-mail: peri at jhmi.edu
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