GCG V. 9.0-GAP

Ellis Golub ellis at vesicle.dental.upenn.edu
Mon May 26 20:03:13 EST 1997


As indicated below, the scoring matricies are indeed the problem.  A simple solution is to add the 
following to your gap commands:  -matr=oldpep.cmp.  This uses the version 8 matrix, and gives the
same fits as version 8.  

Ellis Golub

In article <33898FA4.FF6 at caos.kun.nl>, Jack Leunissen <jackl at caos.kun.nl> writes:
|> Iddo Friedberg wrote:
|> >
|> > I've encountered an interesting phenomenon in GCG v. 9.0, UNIX.
|> > 
|> > Try the following:
|> > gap -in1=sw:lyg_ansan -in2=sw:kad3_bovin  -gap=5 -len=3 -out=out1.pair
|> > gap -in1=sw:kad3_bovin -in2=sw:lyg_ansan  -gap=5 -len=3 -out=out2.pair
|> > 
|> > Now look at the results in files out1.pair and out2.pair
|> > 
|> > Seems like the results are dependent upon sequence order. AFAIK, that
|> > shouldn't be the case in pairwise sequence alignment.
|> 
|> This idiotic behaviour is caused by the comparison matrices that GCG
|> now uses for sequence comparison and alignment. You will see similar
|> (bad) behaviour with COMPARE and DOTPLOT.
|> 
|> The actual cause of the problem are in fact the numbers on the main
|> diagonal in the comparison matrix: these numbers reflect the self-
|> matches of amino acids. In version 8 these numbers were artificially
|> set to one and the same value, in order to facilitate the scoring of 
|> identities.
|> Version 9 now uses the original values on the diagonal, which are
|> different for the amino acids, reflecting the "conservativeness" of
|> amino acids. Correct by itself, for some reason it doesn't work with 
|> the version 9 GCG programs!!!
|> 
|> To illustrate this, you might try the following: manually change all
|> the diagonal values in theOBLOSUM62.CMP matrix to one value (I put
|> them all to 11, which is the W-W selfmatch). Now you will see that
|> the alignment is reasonable, and is the same for both orientations!
|> 
|> One more reason to stick to version 8 for the time being....
|> 
|> Cheers,
|> Jack
|> 
|>    Jack A.M. Leunissen       | Email: jackl at caos.kun.nl
|>    CAOS/CAMM Center          | Tel. : +31 24 365 22 48
|>    University of Nijmegen    | Fax  : +31 24 365 29 77
|>    Nijmegen, The Netherlands | Www  : http://www.caos.kun.nl

--
Ellis Golub                  Phone: (215) 898-4629
Biochemistry Department      FAX:   (215) 898-3695
University of Pennsylvania   ellis at biochem.dental.upenn.edu
School of Dental Medicine             
4001 Spruce Street
Philadelphia, PA 19104-6003




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