Question: Orthologous non-coding genes
0
gravatar for int11ap1
5.6 years ago by
int11ap1380
Barcelona
int11ap1380 wrote:

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.

rna-seq ncrna orthology • 2.2k views
ADD COMMENTlink modified 5.6 years ago by Ares Cao20 • written 5.6 years ago by int11ap1380
1
gravatar for pld
5.6 years ago by
pld4.8k
United States
pld4.8k wrote:

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

 

ADD COMMENTlink written 5.6 years ago by pld4.8k

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

ADD REPLYlink written 5.6 years ago by int11ap1380
1
gravatar for Ares Cao
5.6 years ago by
Ares Cao20
Shanghai China
Ares Cao20 wrote:

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~

ADD COMMENTlink written 5.6 years ago by Ares Cao20
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