[BiO BB] HMMER on genomes

Peri Suraj bioinfo_india at yahoo.com
Mon Jul 28 07:45:39 EDT 2003

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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