[Bioperl-l] BlastPlus -Match/Mismatch scores + Gap costs

[Janine Arloth]

Hello all,

while running blast(n) I want to extend to method_arg like:
..
$result = $fac->$blastprogramm_input(
	-query       => $seq,
	-outfile     => "blast.txt",
	-method_args => [
		"-num_alignments" => $num_alignments_input,
		"-evalue"         => $evalue_input,
		"-word_size"     => $word_size_input,
		"-?"	                   =>	$match_score_input,
                "-?"                     => $gapcosts_input	
.....
	]
);
...

 in Bio/Tools/BlastPlus/Config.pm I found for gap costs: bln| gapopen  and bln| gapextend
so when I have the input  value = "4 4"  , then Existence:  4 = gapaopen  and Extension: 4 = gapextend ??

Is there a similar usage for Match/Mismatch scores like  value="1,-2"  -> match=1 and mismatch=-2??
(I can't find it)

Thanks for help.