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Problem with profilesearch (with a solution)

Heikki Lehvaslaiho Heikki.Lehvaslaiho at csc.fi
Fri Mar 31 07:15:09 EST 1995


Some time ago, our GCG program profilesearch started crashing middle of
searches with an error message:

    Sequence information overflows string buffer!

After some head scratching and a mail message to gcg.com, things were
cleared out.

The problem was there only when the whole SWISS-PROT database was
searched. Profilesearch does something very stupid. It buffers all of the
descriptions as it searches the database and it happens that descriptions
in SWISS-PROT  are longer than in PIR.

To get going again, one has to modify the critical parameter and


!*      The names and description of each sequence is saved in an
!*      array called bigstring.  This is the major item using memory.
!*      If your memory is limited change this so that only the sequence 
!*      entry name is saved, and decrease the size of MaxStrBuff.  

       Integer MAXSTRBUFF
        Parameter (MAXSTRBUFF=4 000 000)

But to what value one should give to MAXSTRBUFF?  The default value
crashed the program at 36 k sequences. I have it now at its maximmum 7
000 000 which should be enough until SWISS-PROT reaches 60 k entries. (It
is currently 43470+483). Luckily, a note from GCG said that they "will
change the way the program handles the documentation for individual
sequences and try to remove the limit of 60,000".


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     _/  _/  _/  Heikki Lehvaslaiho  <Heikki.Lehvaslaiho at CSC.FI>
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   _/  _/  _/  Center for Scientific Computing
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