🚀 go-pugleaf

  Iddo Friedberg writes:
  IF> Hello,
  IF> I've encountered an interesting phenomenon in GCG v. 9.0, UNIX.

I don't know much about GCG, but want to suggest an explanation anyways.
	
  IF> Try the following:
  IF> gap -in1=sw:lyg_ansan -in2=sw:kad3_bovin  -gap=5 -len=3 -out=out1.pair
  IF> gap -in1=sw:kad3_bovin -in2=sw:lyg_ansan  -gap=5 -len=3 -out=out2.pair

  IF> Now look at the results in files out1.pair and out2.pair

  IF> Seems like the results are dependent upon sequence order. AFAIK, that
  IF> shouldn't be the case in pairwise sequence alignment.

My guess that you are seeing to two different alignments, but with the 
same score? If there is more than one alignment with the optimal score, one
alignment is chosen arbitrarily. There can be many equivalent (with
respect to alignment score) alignments. 

	Best regards,
	Lars

-- 
Lars Arvestad            (MIME correspondence welcome)
Dept. of Numerical Analysis and Computing Science
Royal Institute of Technology (KTH), Stockholm, Sweden