HMMER w/ GCG db?

Kevin Karplus karplus at cse.ucsc.edu
Wed Jun 7 16:49:41 EST 2000

In article <8hgvoq$obc at gap.cco.caltech.edu>, mathog at seqaxp.bio.caltech.edu (David Mathog) writes:
|> 2.  There's some sort of memory  problem feeding hmmsearch a really 
|>     large translated database in this manner - I only just today wrote to S. Eddy
|>     about that so don't know the solution yet.  It may or may not affect
|>     Unix systems.  I suspect it will cause the hmmsearch process to use a
|>     lot of memory though.  I also suspect that the problem is related to
|>     the huge "protein" fasta entries which result from just translating
|>     an entire genbank DNA entry.  Since it seems to depend more on the 
|>     composition of the data fed in than on the absolute size of the 
|>     database.

The SAM package provides many of the same features as the HMMer
package (and a number of features not available with HMM).  We have
had no problem with SAM running large databases through the search
programs, probably because SAM uses a space-efficient version of the
fundamental dynamic programming algorithms.

SAM is free to academics and non-profits and is available at
reasonable license fees to corporations.

for more information.

You can also try out some of the uses of SAM for free at 

Kevin Karplus 	karplus at cse.ucsc.edu	http://www.cse.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck
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