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protein MSA from ensembl compara

I see ensembl compara provides genome multiple sequence alignment (MSA). Can we find protein MSA from compara as well? Are there any other pre-computed protein MSA for vertebrate?

ensembl
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updated by GenoMax GenoMax • written by Xiao • Xiao

As a follow-up question, can we download a sub-tree including fewer species? Thanks!

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written by Xiao • Xiao

Yes you can.

Sub-tree

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written by GenoMax GenoMax

1 answer

You can get protein sequences in Wasabi alignments from the gene trees. From a gene tree click on any node then Wasabi viewer to get an alignment.

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written by Emily Emily

Thanks for your answer. Can I know the meaning of * in the MSA? I think it is different from gap '-'? Here is one example when I downloaded the gene tree for ENSG00000211626, there is a * in this protein.

>Mus caroli strain CAROLI_EIJ, Ryukyu mouse, MGP_CAROLIEiJ_G0000075, MGP_CAROLIEiJ_P0000104
-MVFTPHIL----------------GLLLF*ISASTGDILMTQSPATLSVTPGETVSLSCRASQSINKNLHWYQQKSHGSPRLFIKYASDSISGIPSRFTGSGSGTDYTLSINSVKPEDEGIYYCHQCYSTPNN-
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updated by GenoMax GenoMax • written by Xiao • Xiao

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