protein MSA from ensembl compara
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10 months ago
Xiao • 0

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

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Yes you can.

Sub-tree

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10 months ago
Emily 23k

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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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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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

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