I need to do multiple sequence alignment to check one particular gene of one species with other species which also contain that gene. eg. MSTN of Myotis davidii with MSTN of Myotis lucifugus AND many more species having that particular gene MSTN. To find in the phylogenetic tree in which stage, the particular species disappeared.
Please guide me.
Thanks Naresh
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Naresh
2 answers
It may be worth having a look at Ensembl has to offer in terms of MSA. We've got the genome of Myotis lucifugus where the MSTN has been annotated. LastZ genomic alignments have been pre-calculated across 39 vertebrate genomes. This can be viewed on the Ensembl Browser website for example.
Before you do MSA, first start with blast. Take the sequence, and blast across multiple vertebrate and invertebrate species. Compare the hits and see where it emerges/disappears. Then try to make MSA (multiple tools out there; u can try JALVIEW to begin with), by concatenating exonic sequences. Check if introns have some conserved segment.
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What additional guidance do you need? You have described what needs to be done already.
As to how you would infer when a particular species disappeared from looking at such a tree is unclear.
Sir, I need to which multiple sequence alignment will be good to do this and analyse the results.
Please no need to call anyone sir.
If you look at the MSTN uniprot entry for human here and then go down to the phylogenomic databases you can find pre-computed tree for this gene across many taxa. @chirag describes the basic procedure you would want to do below if you want to compute the tree yourself.
NCBI has some pre-computed information as well as sequences available here. Click on the tabs at the top to go from tree to sequences.
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