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.
•
written
by
gurban2013 •
1 answer
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?
Log in to answer this question.
-
How codeml detects positive selection
written by Amay •
-
CODEML: Ideal setting for generating dn/ds values for a gene family within a species.
written by venura
-
RNA-Seq database across rodents
written by qwzhang0601
-
p53 cancer patient RNA seq and protein sequence data
written by sxp358 •
-
PAML NsSites sequence length influences significance?
written by susannak •
-
dN/dS within and between species
written by krc3004 •
-
Should I average dN/dS over all CDS for a gene or consider only the longest transcript?
written by shreyasibiswas88 •
-
Level of selection
written by ibasan •
-
Why Has2 Gene Was Not Annotated As Heterocephalus Glaber (Naked Mole-Rat) In Genebank
written by smagikern •
-
Chromosome Purification Before De Novo Assembly
written by Jeremy Leipzig
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.
Take a look at Ostrow et al, they've detected positive selection in cancer.