One of our users here at Daresbury has reported a problem with BESTFIT when it
it used to compare a short sequence (protein) against a longer one.
When the first sequence is the short one, it works fine, but when the short
sequence is second, it gets confused.
e.g.,
BESTFIT of what sequence 1 ? test1.gcg
Begin (* 1 *) ?
End (* 7 *) ?
Reverse (* No *) ?
to what sequence 2 (* test1.gcg *) ? swiss:p24158
Begin (* 1 *) ?
End (* 256 *) ?
Reverse (* No *) ?
> stuff deleted
Symbol comparison table: /exe1/gcg/gcgcore/data/rundata/swgappep.cmp
> stuff deleted
test1.gcg x p24158 August 10, 1993 11:50 ..
1 DIPQRLV 7
|||||||
75 DIPQRLV 81
> However,
BESTFIT of what sequence 1 ? swiss:p24158
Begin (* 1 *) ?
End (* 256 *) ?
Reverse (* No *) ?
to what sequence 2 (* swiss:p24158 *) ? test1.gcg
Begin (* 1 *) ?
End (* 7 *) ?
Reverse (* No *) ?
> stuff deleted
Symbol comparison table: /exe1/gcg/gcgcore/data/rundata/swgapdna.cmp
> stuff deleted
3 HRPPSPA 9
: | : :
1 DIPQRLV 7
The problem is that it thinks the short sequence is DNA.
The bug is that including -protein on the command line, to force it to think
protein, does not work. The only way round this is to fetch the protein
comparison table and explicitly declare that in the command line.
I have heard that this problem has been reported before and that somebody posted
a fix. If anyone does have the cure for this, could they post or e-mail it?
Thanks for the help,
Lachlan Bell
