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I have a list of mouse genes, but all our analysis happens for human genes. Is that possible to translate these mouse genes to human genes? and is there any tool that can help me on this?

I am mostly a computer science guy, I am not sure this is even possible. However, according to someone, this could happen, I don't expect a full conversion though.


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Your question is a little unclear. Are you trying to find the sequences for the corresponding human genes, or just the name of the human gene? – MattDMo Jan 10 '14 at 18:10
Just the name is fine. Thanks – Haohan Wang Jan 11 '14 at 0:23
up vote 2 down vote accepted

I would recommend using Biomart from Ensembl. This is basically a Swiss Army Knife for converting gene names into various IDs, getting corresponding locations on the chromosomes and so on. You can upload a list of gene names and convert them into the corresponding gene IDs of other species and the convert these IDs back to gene names.

If you haven't used Biomart yet, you can either start by going on their help page or by having a look on this tutorial for the conversion of IDs.

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Yup, use biomart. When you say you have a list, do you have a list of ensembl gene IDs, or a list of Gene Symbols, or Refseq IDs? The gene symbol is probably what you want; the name that you will be able to find in both genomes ("Cdh23" or "ApoE1" are examples). But of course there will be some mouse genes that aren't in humans, and vice-versa. – swbarnes2 Jan 10 '14 at 22:15
What I have is gene symbols. Thank you. – Haohan Wang Jan 11 '14 at 0:27

Sounds like you are searching for homologs of mouse genes in human genome. BLAST should be able to help you finding that. You might want to find the sequences for the mouse genes on GenBank and run BLAST against it.

However, in this scenario, protein BLAST (BLASTp) will actually helps you more since the protein sequences are conserved better than DNA sequences are between species. In this case, you need to find the proteins coded by the mouse genes, and run BLASTp then.

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Depending on how long the list is, you don't want to use Blast. Biomart (once you learned how to use it) is a really good tool here. – Chris Jan 10 '14 at 22:42

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