What information can I extract from a large dataset of a single gene

TinySci · 05-13-2015, 07:32 AM

Hello!

I am working with a lab that has amassed a relatively large dataset (>1,000 samples) of a single gene sequence (rpoD from Aeromonas spp.). They have deduced phylogenetic information using MEGA, but I am wondering what else can be learned from using this data?

Has anyone been in a similar situation?

Thank you in advanced!

jwag · 05-13-2015, 10:01 AM

You might be able to look at amino-acid (codon) specific positive selection, although this might work better if you find the gene in multiple other species for comparison. You might also be able to look at rates of evolution (molecular clock) of the gene.

TinySci · 05-14-2015, 02:26 AM

jwag,

Thanks for the suggestions. Could you provide literature for these types of investigations?

jwag · 05-14-2015, 10:55 AM

Codeml software for looking at positive selection seems to be pretty popular, which is part of the PAML package. There's a few tutorials online that you can look at.

http://abacus.gene.ucl.ac.uk/software/paml.html

For molecular clock investigation, I'm less familiar with that because I haven't had a dataset suitable for it. Though I do know that MEGA can do molecular clock tests.

You could also try out TreeSAAP to test for functional changes.

http://dna.cs.byu.edu/treesaap/

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05-13-2015, 07:32 AM	#1
TinySci Junior Member Location: Spain Join Date: May 2015 Posts: 5	What information can I extract from a large dataset of a single gene Hello! I am working with a lab that has amassed a relatively large dataset (>1,000 samples) of a single gene sequence (rpoD from Aeromonas spp.). They have deduced phylogenetic information using MEGA, but I am wondering what else can be learned from using this data? Has anyone been in a similar situation? Thank you in advanced!

05-13-2015, 10:01 AM	#2
jwag Member Location: USA Join Date: Apr 2013 Posts: 42	You might be able to look at amino-acid (codon) specific positive selection, although this might work better if you find the gene in multiple other species for comparison. You might also be able to look at rates of evolution (molecular clock) of the gene.

05-14-2015, 02:26 AM	#3
TinySci Junior Member Location: Spain Join Date: May 2015 Posts: 5	jwag, Thanks for the suggestions. Could you provide literature for these types of investigations?

05-14-2015, 10:55 AM	#4
jwag Member Location: USA Join Date: Apr 2013 Posts: 42	Codeml software for looking at positive selection seems to be pretty popular, which is part of the PAML package. There's a few tutorials online that you can look at. http://abacus.gene.ucl.ac.uk/software/paml.html For molecular clock investigation, I'm less familiar with that because I haven't had a dataset suitable for it. Though I do know that MEGA can do molecular clock tests. You could also try out TreeSAAP to test for functional changes. http://dna.cs.byu.edu/treesaap/