In <1992Feb6.082209.9796 at urz.unibas.ch> doelz at urz.unibas.ch writes:
> In article <1992Feb5.202309.22818 at coe.montana.edu>, umbjs at cs.montana.edu (Jean Starkey) writes:
>> > significant homology. I have used FASTA and BESTFIT
> > and other programs on the GCG package available on
> > the front end of the Pittsburg super computer.
>> If there is Version 7 of the GCG program software installed this
> contains the program PILEUP which gets you what you might need.
>> The question is just whether you're trying to align garbage or whether
> there's really a piece of common information in it. No computer can help
> if the desired homology doesn't exist. Unfourtunately, the computer
> won't tell you, but PILEUP will give up if you have more than 2000 Gap
> insertions.
>> regards
> Reinhard
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> Dr. Reinhard Doelz * EAN doelz at urz.unibas.ch> Biocomputing * DECNET 20579::48130::doelz
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In trying to decide between meaningful homology and garbage, also note that
GCG7's BESTFIT has an optional parameter ( /RANDOMIZE=n ) that provides a mean
and std.dev. for n comparisons where one of the sequence pair is randomized.
If the score for the nonrandom alignment is 'significantly' greater than the
mean ( Anyone remember the criteria for significance from ALIGN scores used in
the 'old days'? Wasn't it 3 SD above mean for 95% degree of confidence?), then
you've got reason to be doing alignments; if not, don't bother using any more
cpu time.
MJW
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