What kind of BLAST to use in Gene Ontology?

Question

[l.souza]

Hello everyone,

I am performing a Gene Ontology analysis with the proteins obtained by a Proteomics experiment. To achieve the gene ontology I choose to use Blast2GO; however, I got a doubt regarding using blastp or tblastn in this analysis.

When using tblastn, I got hits with species pretty distant with a poor alignment around 50-60% (This is expected considering the codon degeneracy of the genetic code). When using blastp the major hits are with the species of interest, or within the same family.

So, I would like to know if somone has some thoughts regarding the use of this two options.

Best regards,

Lucas!

Answer 1

[Bill Pearson]

You should use BLASTP. It will have fewer false positives and higher sensitivity.