Genbank FASTA server -> NCBI?

cherry at OPAL.MGH.HARVARD.EDU cherry at OPAL.MGH.HARVARD.EDU
Wed Sep 30 23:54:36 EST 1992


>In article <28SEP199211032524 at seqvax.caltech.edu>, mathog at seqvax.caltech.edu (David Mathog) writes:
>>Dennis Benson's reply to my post:
>>>  The primary reason is machine resources.  We have BLAST running
>>>  on a parallelized version of an 8-processor Silicon Graphics.
>>>  This provides very rapid turn-around for searches and allows us
>>>  to handle the daily load of between 1000 and 2000 searches per
>>>  day, including hundreds of BLASTX and TBLASTN searches which are
>>>  heavily CPU-intensive.  We simply would not have the capacity to
>>>  accommodate FASTA searches in addition to this machine load and
>>>  still provide reasonable response times.
>>
>>Here we go again.  In the bad old days we ran local FASTA's on our
>>VAXstation.  Then we offloaded these jobs to the Genbank FASTA server.

I saw nothing in your message about why you do not use the BLAST
server.

For about the last year BLAST searches have all but replaced FASTA
searches here at Massachusetts General Hospital. I don't have any
problem with the FASTA server going away because we didn't use it and
a great alternative is available (blast at ncbi.nlm.nih.gov).

I think you greatly underestimate the amount of horsepower required to
setup one of these servers. FASTA takes a lot of CPU time.  Opening a
mail server requires that you can provide and support the service for
the future.

Mike Cherry 

P.S. I also think your economics of computer purchases is flawed.  Any
computers or periferals that are purchases are used for much more that
just sequence searches. Plus in the example of a lab buying a CD-ROM
drive there are several other diskes that are available and quite
useful. In some cases not available via any other media: eg. the NCBI
Entrez CD-ROM, PIR Atlas disk and some hardware vendors routinely
provide software updates on CD.




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