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7

Your question could be phrased more specifically to avoid ambiguity, but rephrasing it the way that I suspect you mean it, ("Is there any evidence showing that [the rate of] copy number variation changes over time?"), then yes, there is indeed. The rate depends on many factors including which mechanism and which organism and which region of the organism's ...


6

I've found a nice review that has many details on plasmid replication in general, and several papers about pSC101 in detail, and I'll try to extract the key information from these papers. First of all your plasmid as an ori region that contains so called iteron: In many cases, the origin of replication contains directly repeated sequences, termed ...


5

Allelic imbalance is a pretty broad phenomenon difference in the expression of two alleles. As such you have listed would probably cause allelic imbalance, but it could be the result of methylation or even differences in RNA sequences between the alleles which say interfere with post translational splicing say. In the case of copy number variations, if a ...


4

A copy number variation (CNV) is when the number of copies of a particular gene varies from one individual to the next. From: the NIH Glossary Focal CNVs are regions of repeated genetic information that only span a small proportion (<25%) of the chromosome arm (although this does not seem to be a consistent rule), and can contain few genes. ...


4

I'd take that computational angle and run the sequence data through tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964). Ideally, you'd install this locally. This tool is what the UCSC folks use and it has been the best known, most widely used tRNA predictor for years. It's what we all used on Arabidopsis thaliana genome annotation back in the late ...


3

A database that answers the question, charting telomere repeat sequences for all known species, is: http://telomerase.asu.edu/sequences_telomere.html For example in Yeast:


2

Yes, one sample can contain different alterations. For each patient there is typically one tumour specimen that is removed. That specimen may be divided up into several samples (e.g. one for DNA sequencing, one for RNA sequencing, one for methylation microarray, and one for copy-number variation microarray), however each sample contains thousands of ...


2

I would use an RNA microarray to look at those difference instead of sequencing. To delicately amplify your tRNAs in an unbiased manner would be a tricky molecular biology endeavor. I wouldn't be surprised if there were detectable and significant differences. Those experiments will be able to confirm your hypotheses regarding codon usage bias.


2

TTAGG telomeric repeats have been found in several insects. From Sahara, Marek & Traut (1): (TTAGG)n-containing telomeres were found in three Lepidoptera species, the silkworm Bombyx mori (in which the telomeric sequence was recently discovered), the flour moth Ephestia kuehniella, and the wax moth Galleria mellonella, in one species of ...


1

There are many methods for the analysis of CNV. If you are an R user I would recommend you to take a look at the Bioconductor package list, in particular the section for copy number variation. Currently it contains 50 packages!


1

Your suggested approach of comparing to the baseline distribution on a point-by-point basis isn't bad, although it's going to be susceptible to small false positives from noise. You'd probably want to only use events that span a certain minimum number of consecutive observations. You might also want to look into circular binary segmentation, as described ...



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