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
