10 votes
Accepted

Can exons be located outside of the coding sequence?

Yes, of course. Exons are not limited to the protein coding regions. Many UTRs are in exons. In fact, you even have various cases of UTRs being multiple exons, and being spliced. What is strange in ...
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  • 8,160
7 votes
Accepted

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

Sulfur atoms are shown in yellow. The molecular viewer that you use is JSMol (JMol ported to the web). Atoms are colored by element: grey C, blue N, red O and yellow S. If you wonder how other atoms ...
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  • 1,091
7 votes

Can exons be located outside of the coding sequence?

Those are the untranslated regions (UTRs). All mRNAs have a 5' UTR and a 3' UTR. These give the ribosome something to grab onto and often contain important regulatory sites such as miRNA target sites.
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2 votes

LD analysis in PLINK based on reference and a SNP list

It looks like the first command is calculating pairwise linkage disequilibrium r2 between your SNPs. The second command is clumping your dataset based on a p-value over a file of association test ...
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  • 393
2 votes

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

Here is how we do this: First break your gene model down into non-overlapping chunks, such that any possible gene model can be built from a combination of those chunks. E.g. ...
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  • 3,221
2 votes

Are there any Sulfur Dioxide molecules in this structure?

The answer, as provided in the comments by gilleain is No. The commenter wanted to know why I asked this. The reason is I heard sulfur dioxide as silent speech when thinking about antibodies that’s ...
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  • 153
2 votes

Can exons be located outside of the coding sequence?

Although the explanation that UTR (untranscribed) regions can consist of multiple exons covers most situations, I think it is good to mention stop codon readthrough. This would result in a CDS (...
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1 vote

Installing modules in perl for Circos

The simplest solution is to install conda/Anaconda Then type any one of the following. Start with the top command and if it is unavailable go to the next commend down - only needs work once: ...
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  • 7,756
1 vote

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

Not in the way you suggest: a sequence of letters with the property of being immutable by any type of permutation on its constituent bases. I would be interested if anything of the likes exists in ...
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  • 353
1 vote

Power calculation for GWAS/EWAS

Interesting question I would recommend the effective population size $N_{e}$, and error bars around this. Ne can be calculated via $F_{st}$ and is perhaps the most important parameter to determine ...
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  • 7,756
1 vote

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

@Michael's comment is correct but possibly a little difficult to understand, so I'm going to rephrase it here with an example (please let me know if I'm misrepresenting): This matrix (pretending for ...
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1 vote

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

Essentially you are comparing a "local clock" with a global clock and whether the instance rate relates to the global it depends on the model and in MCMC clocks in most cases the answer is no. A ...
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  • 7,756
1 vote
Accepted

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

The ultimate choice stems from your individual interests and not a scientific reason... but having said that some pointer of issues may be handy. I am assuming that you want to make an inhibitor that ...
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  • 3,719
1 vote

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

Did you look into literature? I am not an expert in this field, but a small search on google leads me to IRFinder (ref.), a tool that can assess intron retention. My advice is to see if this tool can ...
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  • 3,551
1 vote

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

It is not trivial getting MB to run in parallel because from my experience it required privileges that regular uses didn't have. I did this via MPI but ran it across a cluster in superuser mode. ...
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  • 7,756
1 vote

Unable to Install PGDSpider using Ubuntu and wine

Don't use Wine at all! You seem to be running an Ubuntu installation inside a MacOS system using parallels. And then a Windows emulation layer (wine) on top of that. This is a very complex system. ...
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  • 8,160
1 vote

How to confirm exon shuffling in a gene?

These suggestions are based on your comment that you have the gene sequence. For a statistical approach, you could formulate a null model and show that the sequence similarity you observe is much ...
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