Local blastp option -qcov_hsp_perc

Question

[fec2]

Hi all,

I need to performed blastp for 2 genome (against each other). According to the paper, I need to get the number of protein which has "alignable region of the query protein sequence of more than 50%".

For Blastp option, -qcov_hsp_perc should mean Percentage of Query Coverage Per HSP, right? Therefore, if I perform blastp with option "-qcov_hsp_perc 50" mean I only select alignable region of the query protein sequence of more than 50%?

Thank you.

[h.mon]

You want to align two genomes, or two sets of proteins?

[fec2]

Ya, 2 sets of proteins. I am using -subject option of blastp.