Blastn doesn't allow certain gap penalties?

Question

[colin.kern]

I'm trying to follow a procedure described in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716261/

Specifically their parameters for BLAST which they say are "match = +5, mismatch = -4, gapopen = 10, gapextension = 10". However when I try to run blastn with these parameters, it doesn't let me use them, saying

BLAST engine error: Error: Gap existence and extension values 10 and 10 are not supported for substitution scores 5 and -4
10 and 6 are supported existence and extension values
8 and 6 are supported existence and extension values
25 and 10 are supported existence and extension values
Any values more stringent than 25 and 10 are supported

Why doesn't it allow these parameters? Is it likely that the paper has a typo in the parameters they report, or did older or alternate version of BLAST support these?

[thackl]

What version of BLAST are you using? The paper is from 2007, they most likely used a different BLAST version. BLAST+, which you probably have hasn't been around before 2011 (blast+ releases). A likely 2007 BLAST version would be BLAST-2.2.16 or so (legacy blast releases). Legacy BLAST was more flexible regarding scoring and gap parameter settings - I don't know exactly though, whether your scoring model will work...

Answer 1

[lmnganga]

I answer a year later but hopefully it's going to help someone else.

Certain combinations are not allowHere are the allowed combinations as defined by the official BLAST manual.