Question: Which multiple sequence alignment tool works best to compare mutations in a gene in multiple species?
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gravatar for Naresh
3.6 years ago by
Naresh60
Korea, Republic Of
Naresh60 wrote:

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

alignment • 1.9k views
ADD COMMENTlink modified 3.6 years ago by Sukhdeep Singh9.9k • written 3.6 years ago by Naresh60
1

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.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by genomax74k

Sir, I need to which multiple sequence alignment will be good to do this and analyse the results.

ADD REPLYlink written 3.6 years ago by Naresh60

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.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by genomax74k

Welcome to Biostars. Try to formulate a succinct and informative question title for your future questions.

ADD REPLYlink written 3.6 years ago by Sukhdeep Singh9.9k
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gravatar for Denise - Open Targets
3.6 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

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.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Denise - Open Targets5.0k
0
gravatar for Chirag Nepal
3.6 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

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.

ADD COMMENTlink written 3.6 years ago by Chirag Nepal2.2k
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