Finding a orthologous genes between human and mouse along with percent alignment?

Question

[wangfx]

Hello,

I was wondering if it was possible to find all orthologous genes between mouse and human, and then getting something along the lines of sequence alignment percentage or score between the two species. I have tried biomart, which works well 80% of the time, but there are also genes that don't have a orthologs between human and mouse according to biomart but do according to other databases. Is there a more concise/complete database form where I could pull this data from?

Thanks!

Answer 1

[Jean-Karim Heriche]

Have you tried TreeFam ? You can get all pairwise homologs for any two species from the download page. You can then use the API to get alignments. Note that the procedure used by Ensembl is similar (if not the same) as the one used by TreeFam so the results should be almost identical. Also I don't know what other databases you've looked at but some may not be entirely correct. I would have higher confidence in a resource that infers orthologs from a phylogenetic tree than in one that does it using reciprocal best hits.

Answer 2

[GenoMax]

Have you looked at this page. It has a complete list of human/mouse homologs.