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Old 09-15-2012, 05:31 AM   #1
xhuister
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Location: China

Join Date: Apr 2010
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Default Find orthologous regions (not just genes) between two species?

Hi all,

I want to find orthologous regions between Medicago truncatula and Arabidopsis thaliana. Or to convert the coordinates from one species to another.

I found that liftover can convert the coordinates between assemblies. But I'm afraid that it is not suitable for converting coordinates from Ath. to Mtr. Because there are 5 chromosomes in Ath. but there are 8 chrs in Mtr, I don't know how liftover can deal with this issue and there is no chain files for Ath. or Mtr. (I have not used liftover yet.)

So I may need to find the orthologous regions (including genes and non coding regions) instead. Is there any tool for locating orthologous regions between two species? And is there any database that I can download the ortholog genes between Ath. and Mtr?

Thanks!

Xiaohui
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Old 09-15-2012, 11:58 PM   #2
klaas.vandepoele
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Default

Dear Xiaohui

The PLAZA comparative genomics can partially address your question. See http://bioinformatics.psb.ugent.be/plaza/

Please have a look at this dotplot to explore gene colinearity between Ath and Mtr. http://bioinformatics.psb.ugent.be/r...ot_AT_MT_3.png

As you well see, the highly diverged nature of both species result in the absence of a simple 1:1 orthology relationship at the genome level.

For a specific gene of interest, you can use the Integrative Orthology Viewer to search for orthologous genes incl. conserved genome organization (see anchor point criteria). For more info, please check http://bioinformatics.psb.ugent.be/k...hologous_genes

Alternatively, the WGDotplot or Synteny Plot might also be of interest.

Klaas Vandepoele
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Old 09-17-2012, 09:13 PM   #3
xhuister
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Thank you very much, Klaas! PLAZA seems to be a good resource to compare plant genomes.
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