Annotating putative novel protein sequences - finding orthologs

Question

[Ian Fiddes]

I am working on annotating a few hundred transcripts that may or may not be novel. It is likely that most are orthologs that I was unable to detect via genome alignment, while a couple may be truly novel or have a more distant ortholog. To approach this, I have been running blastp locally against the nr database. However, this is incredibly slow. I need something faster. What do people recommend for this? I looked at OrthoMCL, but that requires having a mySQL database that I can write to.

Answer 1

[natasha.sernova]

There is OMA-program for finding orthologs.

The speed depends upon different factors, see the manual below.

OMA user manual:

http://omabrowser.org/standalone

or in Manual folder as pdf

Also see this following post:

Roary pan genome analysis error

Roary works fast, as authors promise. I've never run it by myself.