Protein scoring matrices in GCG 9

Francois JEANMOUGIN pingouin at crystal.u-strasbg.fr
Wed Mar 19 09:07:05 EST 1997

In article <5gods4$8oc at lyra.csx.cam.ac.uk>,
	tjrc1 at mole.bio.cam.ac.uk (Tim Cutts) writes:
> Hi people,
> I have had a number of queries from users on my system about what
> appears (to them) to be major differences between the output from pileup
> in GCG 8 and GCG 9.
> This seems to be due to the new default scoring matrix; does anyone
> know what the rationale was behind this change, and why does it
> produce such different answers to the previous GCG version?  This
> seems to have confused a lot of users.  Of course I can tell them to
> use -matrix=oldpep.cmp if they want the same results as GCG 8, but how
> should they determine which is the appropriate scoring matrix to use?

	There was a discution in the GCG meeting at EMBL Heidelberg, 
where most users were asking for better matrices for PileUp. Perhaps
will this show to your users that a good scoring matrix (or even better
is a set of good scoring matrices) is very very important to make good 
alignments, and make them think on how to improve the quality of the 
alignment (AMAS from Geoff Barton group should be a good tool for that).

	However, I would advice you to make them switch from PileUp
to ClustalW or even better to ClustalX, which can easily be integrated
in the extension menu of seqlab (config file can be sent upon request).
	The latest version seems to be quite stable now and some improvements
and analysis capabilites will be added. Stay tune because the really
stabilized version will come soon (also, Julie just puts the
last beta version when I'm writting this...).


ClustalX require the NCBI tool-kit to compile, sources and static binries
are available via anonymous ftp at :
Francois Jeanmougin
Service de bioinformatique / bioinformatics service
IGBMC BP 163 67404 Illkirch France
tel :(France) 03 88 65 32 71 / (international) (+33) 3 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr
C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun (Thiefaine)

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