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.

See
	http://www.cse.ucsc.edu/research/compbio/sam.html
for more information.

You can also try out some of the uses of SAM for free at 
	http://www.cse.ucsc.edu/research/compbio/HMM-apps/HMM-applications.html

-- 
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
Anything below this line is junk added by others without my approval.







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