GCG V. 9.0-GAP

Tim Cutts tjrc1 at mole.bio.cam.ac.uk
Wed May 28 03:13:26 EST 1997

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:
>[...]             .         .         .         .         .
>>                                           |                
>>        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
>							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.


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