Best way of mapping homologous (non-coding) regions across organisms
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5.7 years ago

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!

Assembly genome alignment sequence blast • 1.1k views

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