[Biojava-l] SimpleGapPenalty defaults

[Khalil El Mazouari]

Hi all,

while doing PSA or MSA with default gop and gep values I obtained the following alignment!

QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS
QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCA---------------------R

Expected PSA should be at least
QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS
QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCA-----R----------------

this expected alignment was obtained with gop=1 and gep=100

I can't understand while the PSA algorithm with default values always adds many gaps at the end of alignment to end up with a S:R while it is obvious that with less gaps we could obtain better SequencePair with R:R?

Finally, how to get a score for PSA, that reflects the number of identical, similar residues and gaps?

Many thanks.

Khalil