[Posted and mailed]
In article <33e48227.9371298 at news.su.se>,
ev-michael at SPAMSTOPnrm.se (Mike Noren) writes:
[...]
> ClustalW 1.6 usually does an acceptable job, even with sequences rich
> in gaps. With sequences of very different lengths it tends to fail
> miserably, though, and I'm not sure how it'll handle very small
> sequences like yours. Profile alignment usually works in v1.6, which
> was not the case in v1.5.
[...]
ClustalW is now version 1.7 and accepts GCG9 multiple sequence
file formats (MSF/RSF) as input. Also, we have done some improvements on
the alfgorithm, especially for highly divregent sequences. ClustalW1.6
has a bug in the GOP calculation and misplaced some residues at
gap opening positions.
Please update your programme from :
ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
Also, give a try to ClustalX (1.5b), which is a GUI for ClustalW
and has some analysis tools.
Feel free to contact me for any question.
François.
--
François Jeanmougin | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
"Ce sont des désespoirs d'intellectuels ennuyés, ou des ennuis
d'intellectuels désespérés, comme vous voulez, comme vous voulez" M. Benin
