Blast+ Nucleotide "-Matrix" Command

Question

[mmlotaief]

HI, I've been trying to run a nucleotide blast (blastn) using BLAST+

here is what it should look like using legacy blast:

blastall -p blastn -d db -i fasta.fasta -o output.blastn -e 10000 -F F -a 7 -M PAM70 -W 7 -a 8 &

and this is the command (as far as I can figure out) using BLAST+ blastn

blastn -task blastn -db db -query fasta.fasta -evalue 10000 -dust no -word_size 7 -matrix PAM70 -num_threads 8 -out output.blastn &

I've also attempted to use the "legacy_blast" script (also legacy_blast.pl) to check if I get the same error...

legacy_blast blastall -p blastn -d db -i fasta.fasta -o output.blastn -F F -M PAM70 -W 7 -a 8 &

Now, on any of those occasions I get this error:

DESCRIPTION Nucleotide-Nucleotide BLAST 2.2.26+

Use '-help' to print detailed descriptions of command line arguments ======================================================================== Error: (CArgException::eInvalidArg) Unknown argument: "matrix" Error: (CArgException::eInvalidArg) Application's initialization failed Program failed, try executing the command manually.

after checking the options for blastn, (and manual) I find there is no -matrix option for blastn. The question is now WHY? Assuming that I can do this and execute it using legacy blast (blastall) why is the same command unable to work for BLAST+? Also, how much faster would using blast+ using this method (provided I can use a nucleotide blast with a PAM70 matrix) be compared to legacy blast ...

Any help is much appreciated. Cheers.

Answer 1

[Torst]

PAM70 is an amino acid subsitution matrix. It makes no sense to use it for nucleotide alignment! That's why blastn does not have -matrix option. The blastp command does have the -matrix command.

You can learn more about these matrices here: http://en.wikipedia.org/wiki/Substitution_matrix