Multiple alignment of protein sequences

WEISE at gandal.dnet WEISE at gandal.dnet
Thu Feb 6 09:13:56 EST 1992


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 
> 
> 
> ************************************************************************
>     Dr. Reinhard Doelz            *     EAN     doelz at urz.unibas.ch
>       Biocomputing                *     DECNET  20579::48130::doelz
> Biozentrum der Universitaet       *     X25     psi%022846211142::embnet
>    Klingelbergstrasse 70          *     FAX     x41 61 261- 6760 
>      CH 4056 Basel                *     TEL     x41 61 267- 2076 or 2247   
> ************************************************************************

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

   _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
 /     Michael J. Weise, Ph.D.    \Univ.of Ga. BioScience Computing Facility \
( weise%gandal.dnet at server.uga.edu \ Dept.of Genetics  UGa, Athens  GA  30602 )
 \ _ _ _'Tis_only_me_speak'n._ _ _ _\_ _ _ _ _ _(404) 542-1409 _ _ _ _ _ _ _ /



More information about the Proteins mailing list