Do blastx and blastp calculate score differently?

Question

[Seq225]

Hi,

I am doing horizontal gene transfer (HGT). My pipeline is based on blast bit-score. So far, I have used blastx (query is a set of my assembled transcripts). Now, I am thinking to use blastp (query is the set of all the translated-ORF from my assembled transcripts).

I am not sure if blastx and blastp will give different bit-scores. I understand that blastx first find the translated-ORF from all frames then run blastp: Am I wrong?

Thanks very much!!

Answer 1

[natasha.sernova]

See this post.

Blast raw score calculation

and the reference to a useful book at the bottom.

It talks about Blast details.

There were also other posts, that deal with your question:

please share your experience for ORF prediction +blastp instead of doing blastx

which one is better to do, blastx or blastp?

Comparable E-Value Among Blast Programs

Why there is some discrepancy between blastx and blastp outputs?

ORFs from blastx results

From my experience, scores are different,

blastx worked better for my problems,

but Blast is an enigmatic tool and

the conclusion depends upon your particular task.

[Seq225]

Wow! Great!! Thanks a ton!!!