In article <5mgpf6$ivr at lyra.csx.cam.ac.uk>,
tjrc1 at mole.bio.cam.ac.uk (Tim Cutts) writes:
> I don't think it's a bug, per se, more a mis-feature.
Sorry, but if I implement such a "mis-feature" in Clustal,
you will mail me it's a bug ;-)...Also, if the order of the
sequences matter, it is also a corruption of the gap algorithm.
> By default, in
> GCG9, gap (and pileup too) does not penalise inserting gaps at the
> ends of the sequences. Consequently putting huge gaps in at the ends
> like this appears to be a good match (duh!). If you use the -endw
> option as well, which enables penalisation of gaps inserted at the
> ends, you might get a more sensible answer.
I will probably (after some tests) alias gap to gap -endw
for my users. This will save some time for me.
Even with the non-weighting gaps, the alignment shown
can't be the highest scoring alignment, or a representant of
the highest scoring family of alignments (look at the quality!).
There is a bug, sure.
Francois Jeanmougin | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
e-mail : jeanmougin at igbmc.u-strasbg.fr
"C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun."(Thiefaine)