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!!
1 answer
See this post.
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?
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.
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