This is a test version of Biostars. For the public version, visit https://www.biostars.org.
convert legacy blast parameters to blastn

Hi all,

I am following the parameters given in a paper for performing blast.

The parameters given are in the old format;

-X 150 -q -1 -F F

Could anyone convert them to the current blastn format?

e.g., (throws errors);

-xdrop_gap_final 150 -penalty -1 -dust no

I could use the old blast, but I am also using

-outfmt "6 std qlen qcovs"

which I don't think is possible for old format?

parameters blast
• 2,845 views • link
updated by Ram Ram • written by c.v.oflynn c.v.oflynn

1 answer

I think the -penalty option might be the culprit. When you change the -penalty value from default, you also need to set the supported values for -gapopen and -gapextend.

You can check the supported combinations here.

• 0 views • link
updated by Ram Ram • written by Siva Siva

Thanks Siva, helped a lot

• 0 views • link
written by c.v.oflynn c.v.oflynn

Log in to answer this question.

More posts like this