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?
As a follow-up question, can we download a sub-tree including fewer species? Thanks!
Yes you can.
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.
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
The * denotes a STOP codon. You can see the TGA codon in the cDNA sequence on the following page:
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