Orthologous non-coding genes

Question

[int11ap1]

Dear all,

I am doing an RNA-seq project, whose aim is to look for lncRNAs of different species. Once I have a set genes that give lncRNAs across different species, I would like to know which genes are orthologous. For proteins, I know that there exists OrthoMCL. However, no idea regarding orthology studies of non-coding genes. Do you know anything about it? There are some tool to use? If not, what do you recommend me to do? Any pipeline?

Thanks in advance.

Answer 1

[pld]

I'm doing the same thing, however I'm just planning on using the best reciprocal blast hits approach. I'm honestly not really sure how valid of an approach it is, it was more a curiosity. A quick PubMed search seems to show most people are aligning against other lncRNAs or against genomic regions in other species, so it seems like sequence alignment is a valid approach.

There are plenty of tools out there that implement best reciprocal blast hits. http://ged.msu.edu/angus/tutorials/reciprocal-blast.html

[int11ap1]

I'm trying to do so with BlastR and a custom script I've written to parse the results of Blast...

Answer 2

[Ares Cao]

i've tried inparanoid to find ortholog between mouse and human and calculate the Ka/Ks, u can have a try~, but it need to do blast first~