Question: Best way of mapping homologous (non-coding) regions across organisms
gravatar for peer_wuensche
4.3 years ago by
peer_wuensche10 wrote:

Dear Biostars,

I would like to find the homologue of a genomic region "A" (can be any size) in another organism/species, in my case this would be human in mouse.

I found a couple of posts touching on the same topic, but in my opinion they don't reach to a satisfying conclusion. To my understanding there are various programs that are supposed to do that, but which one would be the most accurate and yet most flexible (setting cutoff scores etc.) for such a task?

So far I found:

  • liftOver - designed to do this between builds rather than species, so maybe not the best choice
  • pslMAP - good choice according to this post?
  • orthoMAP - whats the difference here?
  • .axt files - can I use pairwise alignment files to filter for the regions of interest?

Btw, my input can be .bed format or a fasta file, I have both. I have to map 130,000 regions from human to mouse.

Since I am very new to the deep space of genomics and bioinformatics, please consider your "obvious" to be a lot less "obvious" in my universe. :P

Your help is highly appreciated!

ADD COMMENTlink written 4.3 years ago by peer_wuensche10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2497 users visited in the last hour