In article <1994Nov9.143225.1 at wehi.edu.au> robert at wehi.edu.au (Robert Flegg) writes:
> GCG provides a number of profiles for use with the PROFILESEARCH and
> PROFILESCAN programs. These profiles have been created by the
> PROFILEMAKE program, as reflected in the header of KINASE.PRF which
> is reproduced below.
>> My question is - Does anybody know what are the sequences and database
> entry numbers of the seven sequences that have been
> used to construct this profile?
>> > (Peptide) PROFILEMAKE v4.00 of: @kin.fil Length: 310 Sequences: 7
> > MaxScore: 193.70 22-JUL-1988 15:49
> >
> > Gap: 1.00 Len: 1.00
> > GapRatio: 0.33 LenRatio: 0.10
> >
> > okbog.frg From: 1 To: 310 Weight: 1.00
> > okbo2c.frg From: 1 To: 310 Weight: 1.00
> > kiboc.frg From: 1 To: 310 Weight: 1.00
> > tvhuf6.frg From: 1 To: 310 Weight: 1.00
> > tvhums.frg From: 1 To: 310 Weight: 1.00
> > a24169.frg From: 1 To: 310 Weight: 1.00
> > a24673.frg From: 1 To: 310 Weight: 1.00
> >
> > Symbol comparison table: ProfilePep.cmp FileCheck: 975
>> I was unable to find any reference to the seven fragments, either online or
> in the GCG documentation. If it is there, and I missed it, then naturally
> I apologize - perhaps I should clean my glasses more often.
>> Any help will be greatly appreciated.
The only folk who know the answer for sure are those who built the profile in 1988,
"kin.fil" and the "*.frg" files are (were) on the system where the profile was made.
The full sequences should be in PIR - the names look like PIR entry names
and are indeed available in PIR (release 42).
The last two are accession numbers from PIR. These now have entry names TVMSP1
and TVHUFF.
You can find the subsequences with profilegap and then use PileUp to get at least close
to the original alignments.
--
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Peter Rice | Informatics Division
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