all against all matching of some 1000 proteins

khofmann at khofmann at
Mon May 17 08:12:31 EST 1993

Dear Netpeople,

In the course of the construction of a specialized sub-database of 
protein informations (based on swiss-prot), I have the following problem:

It is necessary to group about 1000-1500 of proteins (all contained in
swissprot) into families of related sequences. The criteria for the
similarity grouping can be fairly simple, no sophisticated treatment of
borderline cases is necessary.

Two possible solutions for this task come to mind:

- there have been several attempts to do an all-against-all matching of
  SWISSPROT or other protein databases.
  Is there any possibility to access a subset of the matching scores?

- I could do an all-against-all matching of the proteins of interest
  myself, although I have the impression that with 1500 sequences this
  could take some time..
  Is there a (more or less automated) system (perhaps an extension of BLAST)
  that lets me do such a thing? I don't like to issue 1500 blast searches
  and parse the output by hand. 
  If somebody has an idea or has done something similar, please share your
  wisdom with me. By the way, I don't have a Cray at hand, the fastest
  computer under my control is a SPARCstation 10 :-)

Many thanks in advance,

Kay O. Hofmann                            Tel.: +49 221 478-6980
Institut fuer Biochemie (med. Fak.)       Fax.: +49 221 478-6979
Universitaet Koeln
Joseph Stelzmann Str. 52          Internet: khofmann at
D-5000 Koeln 41                             khofmann at

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