positive selection project

Question

[gurban2013]

Hi All, i am working on a project and my professor is of NO help what so ever. the guidelines were to create a testable hypotheses on the evolution of a gene family using a phylogenic selection/detecting pipeline. My hypothesis: the FGF5 gene in a naked mole-rat has under gone positive selection from the its closely related species.

the issue is that i barely know where to start. this guy isnt helping at all...

as of now i have the FGF5 DNA sequences from a few different mole-rats from running a blast of the naked mole-rat gene against the genome of the other species. (should i use protein seq instead of dna)

can someone give me direction on what to do next, should i run a multiple sequence alignment? and how can i ultimately prove positive selection? ive read a number of articles on DN/DS which seems to be the best way go about this.

can someone please help me out... i really enjoy this field and and learning more about it. but this professor is such a turn off.

[Biomonika (Noolean)]

What's your timeline for this project? Are you a student? How did you choose this project? You cannot ultimately prove positive selection, only have strong evidence. It will be frustrating to work on this without help, so I would consider switching projects/professors.

[Asaf]

Take a look at Ostrow et al, they've detected positive selection in cancer.

Answer 1

[gurban2013]

I am a student, yes. i personally picked this project. it was not assigned, 1 month timeline. i was going to use JCoDA software but after consulting with a different professor i believe this topic is out of my skill level / time line. because the gene i was going to use has been prove to not be soley responsible for the lack of fur in naked-mole rats (hr gene). i think i am going to go broader and just compare the genes of FGF5, Lhx2, and HR. and look to analyse the protein mutation to see if i can identify 'Noble' protein / amino mutations.

my game plan is to run a BLAST of the three genes (from the naked mole-rat) against similar species and mammals. then run a multiple sequence alignment and create a phylogenic tree.

my next question is. once i run the multiple sequence Alignment what should i do with that data? and how should i go about creating a phylogenic tree... like what model should i use and what data do they take(protein sequences of each gene/per species?