protein MSA from ensembl compara

Question

[Xiao]

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?

[Xiao]

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

[GenoMax]

Yes you can.

Answer 1

[Emily]

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.

[Xiao]

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-

[Ben_Ensembl]

The * denotes a STOP codon. You can see the TGA codon in the cDNA sequence on the following page: https://www.ensembl.org/Mus_caroli/Transcript/Sequence_cDNA?db=core;g=MGP_CAROLIEiJ_G0000075;r=6:67090187-67090748;t=MGP_CAROLIEiJ_T0000104