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