GCG V. 9.0-GAP

William R. Pearson wrp at alpha0.bioch.virginia.edu
Mon May 26 13:42:40 EST 1997

Iddo Friedberg <idoerg at cc.huji.ac.il> writes:
> I've encountered an interesting phenomenon in GCG v. 9.0, UNIX.
> Try the following:
> gap -in1=sw:lyg_ansan -in2=sw:kad3_bovin  -gap=5 -len=3 -out=out1.pair
> gap -in1=sw:kad3_bovin -in2=sw:lyg_ansan  -gap=5 -len=3 -out=out2.pair
> Now look at the results in files out1.pair and out2.pair
> Seems like the results are dependent upon sequence order. AFAIK, that
> shouldn't be the case in pairwise sequence alignment.
> Can anyone please shed some light on the matter? Please email me
> personally as well as to this newsgroup.
> Many thanks,
> Iddo

Because the alignments that produce a given optimal similarity score are
not necessarily unique, e.g. there are two optimal alignments of 


it is not true that a sequence alignment should be independent of the
order of the sequences.  The score should be independent, and in this
case, it seems to be; 4 in both cases.

Bill Pearson

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