Questions tagged [molecular-genetics]

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6
votes
3answers
729 views

Can exons be located outside of the coding sequence?

I have a gff file like this (I edited the name): ...
5
votes
1answer
1k views

LD analysis in PLINK based on reference and a SNP list

I'm new to PLINK and genetics, and getting confused with two PLINK commands for LD analysis: plink --bfile hapmap --r2 --ld-window-r2 --ld-snp-list --ld-window <...
5
votes
1answer
385 views

MrBayes runs as single-core, but hangs when multi-core

I compiled MrBayes v3.2.7 from github, with the configuration options ./configure --without-beagle --enable-mpi. The program is called mb. I tried one of the ...
4
votes
1answer
507 views

How to confirm exon shuffling in a gene?

Note: this question has also been asked on reddit I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, ...
2
votes
3answers
96 views

Calculating p-value for introns which are retained (or not) between 2 conditions

I am trying to calculate p-values and ultimately FDR values for RI introns for 2 conditions of experiment I have(control and knockdown) For every condition I have 3 biological replicates each: 3 ...
1
vote
1answer
109 views

Power calculation for GWAS/EWAS

I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease. I wonder, does anyone has came across ...
1
vote
1answer
43 views

Why do we scale the rate matrix of a substitution model to make the average rate of substitution equal 1?

The matrix of transition probabilities for a substitution model Q over time t is found as follows: $e^{Qt}$. Since Q and t only show up as a product, we cannot distinguish time and rate of change. So ...
1
vote
1answer
40 views

Which of these enzymes is a better target for virtual screening?

I am a MSc student in Applied Biochemistry. For my Masters Thesis, I will be doing some research about finding new potent inhibitors for a specific enzyme of my choice using molecular docking (virtual ...
1
vote
0answers
22 views

Any input as to what to study in order to work into genetic engineering from math background?

Any input as to what to study in order to work into genetic engineering from math background? I have troubles understanding what the "interface" would be between mathematicians and biologists/...
0
votes
1answer
507 views

What does the yellow mean in this image from Virus Pathogen Resource?

What does the yellow mean in this image? It's from https://www.viprbrc.org/brc/
0
votes
1answer
54 views

Relationship between the instantaneous rate of change of a continuous time Markov model and the rate of a global clock model?

If continuous-time Markov models contain a parameter q that denotes the instantaneous rate of change and a global/strict clock model is the overall rate of evolution, how are these two parameters ...
0
votes
0answers
18 views

Is there any genetic sequence, such that, for all the kinds of mutation, it still has a 100% probability to be passed on?

This question is more on the theoretical-encoding side. Given the known kinds of genetic mutation, transposition, deletion, and such, what can be said about genes that would be left untouched by the ...
-1
votes
1answer
299 views

Unable to Install PGDSpider using Ubuntu and wine

I'm running wine v 2.0.3 using ubuntu v. 16.04.2 on a Mac. I'm trying to install a program called PGDSpider2 from here. Essentially the program is supposed to convert different file formats used for ...
-3
votes
1answer
195 views

Are there any Sulfur Dioxide molecules in this structure?

Does the protein structure shown in the JSmol link have any Sulfur Dioxide molecules? In the picture, the Sulfur element is yellow and Oxygen is red (see here) https://www.viprbrc.org/brc/...