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orthologs between mouse and blind mole rat

Are there databases or studies, which mapped blind mole rate protein sequence onto mouse proteins to find orthologs? Thanks

blast alignment
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written by qwzhang0601 qwzhang0601

If you have the all the blind mole rate protein sequences, you can use OrthogMCL online service, and you can extract all the orthologs with mouse

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written by caizexi123 • caizexi123

Thank you. So there is no existing bmr (blind mole rate)-mouse orthlogs, I have to do the mapping myself.

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written by qwzhang0601 qwzhang0601

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

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written by GenoMax GenoMax

No. The online service will do everything. The input is the full protein sequence of blind mole rate, the output is the orthologs groups for each protein. Then you can analyze which of the orthologs groups mouse have.

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written by caizexi123 • caizexi123

Thank you. I tried 3 times to uploaded the blind mole rat protein sequence to OrthogMCL, but each time after about an hour running, it returned me an message, saying "failed due to an error of the server". Not sure what happened.

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written by qwzhang0601 qwzhang0601

1 answer

Proteinortho can be used to generate the orthologs and also paralogs between the species. Additionally synteny information can be used with the help of annotations. Mole-rat protein sequences can be downloaded here

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written by Rohit Rohit

Thank you. But it was for naked mole rat, is there such data for blind mole rat?

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written by qwzhang0601 qwzhang0601

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