In article <5mgml6$ta at news.u-strasbg.fr>,
Francois JEANMOUGIN <jeanmougin at igbmc.u-strasbg.fr> wrote:
>[...Also posted to help at gcg.com...]
>In article <5mfc74$66t at netnews.upenn.edu>,
>ellis at vesicle.dental.upenn.edu (Ellis Golub) writes:
>[...] . . . . .
>> 151 AGNVRSYARMDIGTTHDDYANDVVARAQYYKQHGY............... 185
>> |
>> 1 .................................GASARLLRAAIMGAPGS 17
>> .
>[...]
>> I saw such strange things using GCG9 gap, but had not time
>to work around to see what's happen. I think there is a bug (big one)
>in GCG9 gap. Also, that was with other sequences (but I can't
>remember which ones!!!).
> Could Oxford Molecular (Ooooooops, sorry) GCG look around this
>problem?
> Francois.
I don't think it's a bug, per se, more a mis-feature. 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.
Tim.
