User: evo_genomics

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evo_genomics60
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Posts by evo_genomics

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How can probability cut off value be set for amino acids residues that causes functional divergence by using False Discover Rate (Diverge Software)?
... 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   ...
amino acid protein family divergence written 4.4 years ago by evo_genomics60
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How can I set threshold for amino acid site profile of type1 functional divergence?
... 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 ...
functional divergence gene family diverge written 4.5 years ago by evo_genomics60
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How can I calculate p value for rate analysis of particular lineage?
... 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 ...
p value evolution selection rate analysis written 4.5 years ago by evo_genomics60
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Answer: A: RMSD of a structural superposition
... 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   ...
written 4.7 years ago by evo_genomics60
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Which criteria should be used for the evalution of Protein strucutre ?
... 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 ...
protein structure i-tasser evaluation criteria written 4.8 years ago by evo_genomics60 • updated 4.7 years ago by Biostar ♦♦ 20
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Is protein structure prediction with low query coverage an appropriate method?
... 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 ...
protein abinito structure written 4.8 years ago by evo_genomics60
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can ihs/ehh be applied on specific geographic region population?
... 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 ...
selection ihs/ehhs population genetics written 4.8 years ago by evo_genomics60 • updated 4.8 years ago by Zev.Kronenberg11k
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Can I apply ihs/ehh on snp?
... 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 ...
population genetics ihs selection snp ehh written 4.8 years ago by evo_genomics60
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Comment: C: How can I download snp genotype file from 1000 Genome?
...     Thank you ...
written 4.8 years ago by evo_genomics60
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which software/program is suitable for visualization of PHASE out put files?
... which software/program is suitable for visualization of haplotypes generated by PHASE program? ...
haplotype phase population genetics written 4.8 years ago by evo_genomics60

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