What kind of BLAST to use in Gene Ontology?
1
0
Entering edit mode
5.2 years ago
l.souza ▴ 80

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!

gene ontology protein blast alignment • 865 views
ADD COMMENT
1
Entering edit mode
5.2 years ago
Bill Pearson ★ 1.0k

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

ADD COMMENT

Login before adding your answer.

Traffic: 1380 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6