Question: How To Stores The Query And Frequency Count Ratio Matrix In A File In Blast+
gravatar for estellequan
6.9 years ago by
estellequan0 wrote:

The command to generate a he query and frequency count ratio matrix using nr might look as follows:

blastpgp -i test1.fa -d nr -h 0.0001 -j 4 -C $id$ -Q test1.matrix -a2

I need the $id$, But I can't find the options in psiblast of blast+.

Now, my command to generat a PSSM using blast+ might look as follows:

psiblast -out_pssm my_protein.ckp -evalue 0.01 -out_ascii_pssm ascii_mtx_file -out output_file -num_iterations 3 -query protein.fasta -db nr

However, I also need the $id$ file as generated by blastpgp -C. How to gain it with blast+.

Any help is appreciated, Thank you very much.

blast+ • 1.5k views
ADD COMMENTlink modified 6.5 years ago by Biostar ♦♦ 20 • written 6.9 years ago by estellequan0
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