I'm extremely new to this and I apologize if this question seems naive. I created a database for virulence factors and did BLASTP.
I got the the following values:
qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore
However, according to my reference journal, I need "slen" or length of matching sequence and "qlen" or length of query sequence to be used in a formula to identify the homologous protein. The formula is:
Ha = pident x slen/qlen
Is "slen/qlen" equivalent to "length" already?
or can I just use evalue and pident to identify the best match? Can you recommend a protocol for this?
Thank you!
I got the the following values:
qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore
However, according to my reference journal, I need "slen" or length of matching sequence and "qlen" or length of query sequence to be used in a formula to identify the homologous protein. The formula is:
Ha = pident x slen/qlen
Is "slen/qlen" equivalent to "length" already?
or can I just use evalue and pident to identify the best match? Can you recommend a protocol for this?
Thank you!