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suggestions for new programs

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Wed Dec 7 17:23:31 EST 1994


In <3c20uk$2k1 at mserv1.dl.ac.uk> gwilliam at hgmp.mrc.ac.uk writes:

> We have a large number of users of the GCG package, and a fairly common
> request is for more specific searching programs to produce lists of
> sequence names:
> 
> search for sequences within a length range
> search for genomic or mRNA or coding nucleotide sequences
> search for peptide sequences within a weight range
> 
> Also a very common request is for a program like pretty that produces a
> display of an input nucleotide sequence with its translation, in
> selected frame(s), underneath.  The translation should be optionally in
> 3-letter code. 

Search for sequences within a length range:
  FINDPATTERNS => define a pattern like  <X(X){48,98}X> => should find all
  sequences that are at least 50 in lenght and not longer than 100. There
  is a bug in GCG V7.3 when you use such a pattern but it is supposed to
  be fixed in V8.0.

Search for genomic or mRNA or coding nucleotide sequences
  This depends on the documentation present in the sequence's reference
  section. So this won't fit into GCG very well. Try Thure Etzold's SRS
  instead. But I would like such a program as well.
  
Regards,
  Christoph Gartmann


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