[BiO BB] HMMER on genomes

[Martin Gollery]

Hi Suraj,

Try GeneWise- you can download it at 
ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/

But I will warn you- it is quite slow!

Marty

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. 
> Thanks
> 
> Suraj.
> 
> 
> =====
> Suraj Peri
> Ph.D. Student
> School of Medicine
> Johns Hopkins University
> 600 North Wolfe Street 
> Baltimore, MD 21287
> Phone:410-502-6665 
> E-mail: peri at jhmi.edu
> 
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Martin Gollery
Associate Director of Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
New phone number! 775-784-7042


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