hit length in the tabular blast output

Question

[seta]

Hi all,

I have a basic question, so sorry in advance. I'm getting a bit confused about "hit length" in the blast output (ncbi-blast-2.2.30+). Please kindly tell me how I can get the "hit length" in the blast output in tabular format (-outfmt 6)?

Thanks

Answer 1

[5heikki]

blastp -help

[seta]

I think it is obtained either by the flag of either "alignment length" or "slen", which one is correct?

[5heikki]

Only you can know what you mean by hit length. Length of the subject sequence? Length of the alignment between the subject and query sequence?

[seta]

That's right, actually, the mean of hit length is what I want to know.