Question: Identifying collinearity between genomes
2
gravatar for S
4.8 years ago by
S90
United States
S90 wrote:

Hi,

I am trying to find collinear genes between two genomes. I tried using progressivemauve, has anybody used this for this purpose? The program generates a .backbone file which from reading the tool manual and their webpage seems to be the file that contain the collinear information. However, this file just lists the coordinates of the collinear regions from each genome without detail information (such as chromosome information and strand). Can someone who has used the tool comment on this?

I have also tried using mugsy but I am not sure if there is a way to output the identified collinear blocks. From the steps listed in their paper, it seems that the collinear blocks are used to generate the final alignment and the aligned regions are normally huge. So would each huge aligned region consist of multiple collinear blocks?

I am also experiment with i-ADHoRe 3.0 which seems promising. One thing is that the program requires a a list of gene pair homologs obtained from using all-against-all blast that I am still not sure of. Would this be done by blasting my protein fasta sequences from one genome as a query against the other genome?

I will appreciate any feedback on above approaches and suggestions if one approach might be better than the other.

Thanks!

collinear • 2.5k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by S90

Do you want to extract colinear genomic sequences or do you want to find regions of gene synteny?

ADD REPLYlink written 4.8 years ago by Phil S.660

I think those two would almost give the same results right except that the collinear genomic sequences might include more than a single gene? I would ultimately like to find regions of gene synteny (conservation of content and order).

ADD REPLYlink written 4.8 years ago by S90

for genome colinearity u can check whether mummer gives you what you want. If your draft genome is not in order you can use nucmer from the same suite to reorder it first. For gene synteny I don't know if there is a tool out there, sry...

ADD REPLYlink written 4.8 years ago by Phil S.660
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