User: evo_genomics
evo_genomics • 60
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Posts by evo_genomics
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... I have used Diverge 3 for type1 analysis. Kindly guide me how can I define probability cut off value for amino acids residues that are causing functional divergence (site profile of type 1divergence) by using False Discover Rate (FDR). What maximum value of FDR can be selected ?
Thanks
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written 5.5 years ago by
evo_genomics • 60
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... How can I set threshold for amino acid site profile of type1 functional divergence implemented in DIVERGE 3.0 version?
I am analysing type 1 functional divergence of gene family consisting of four members. The result of type 1 functional divergence shows significant functional divergence (Ө>0 at ...
written 5.6 years ago by
evo_genomics • 60
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... How can I calculate p value for rate analysis of particular lineage? I have used Mega 6 for estimation of dN/dS ratio ?
Kindly guide me.
I have used 5 primates (human. Chimp, gorilla etc) orthologous sequence for rate analysis (dN/dS ) using Li Wu Lu method. Now I want to calculate P value for esti ...
written 5.6 years ago by
evo_genomics • 60
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... RMSD value should be close to zero. Higher the RMSD value, more target structure deviate from template structure. RMSD value of full length structure should be considered
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written 5.8 years ago by
evo_genomics • 60
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... I have constructed protein structure using I-Tasser serve. What evaluation criteria should be used for selection or rejection of the I-Tasser generated model?
I-Tasser results for my protein are as following:
c-score= -0.82, TM-score=0.61, RMSD=11
should I select protein model on these scores or ...
written 5.9 years ago by
evo_genomics • 60
• updated
5.8 years ago by
Biostar ♦♦ 20
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... I am studying the evolutionary aspect of gene family. I want to build the structure of each family member and want to estimate, how much paralogs (family members) are related or distant from each other at structural level.
But I found very low query coverage of target (family member) with template ...
written 5.9 years ago by
evo_genomics • 60
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... can ihs/ehh be applied on a specific geographic region population (i.e African Population) for selection estimation? or can it be applied to mixture of all populations (Asian, African Europe America )?
which of these two methods will be more logical.
thanks
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written 5.9 years ago by
evo_genomics • 60
• updated
5.9 years ago by
Zev.Kronenberg ♦ 11k
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... I am new in population genetics. I am working on a coding region of Human gene. I have found 5 human specific substitutions out of these 1 substitution is polymorphic in human population.
I wanted to know whether I can apply selection test (ihs/ehh) on this snp.
The frequency of ancestral and deri ...
written 5.9 years ago by
evo_genomics • 60
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... which software/program is suitable for visualization of haplotypes generated by PHASE program?
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written 5.9 years ago by
evo_genomics • 60
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