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1

The units here are relative units of intensity. There may be about a picomole of probes on a microarray spot, but the units of intensity are not scaled to the precise concentration of DNA on the spot. There are many variables which make exact measurements of intensity difficult to translate into the number of RNA bound to a spot. The main one is ...


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The codon usage biases are species-dependant, so you may have to measure it for the genome or set of genes you are interested in. This bias is at least in some cases correlated to the genome composition in terms of A, T, G and C (see figure 3 of this paper about cyanobacteria). So in a sense, it is indeed dependent on the context if you include nucleotide ...


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The phenomenon of using different codons with different probabilities is called codon usage bias. How the different codons are used is sometimes pretty different between species and requires some care. This is especially true when you want to overexpress sequences in bacteria to produce protein, which may need codon optimization to ensure an optimal codon ...


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I'm assuming you mean DNA sequencing (excluding things like RNA-seq). Is Sanger sequencing the first generation? From Metzker 2010: The automated Sanger method is considered as a "first-generation" technology Some of the technology that was in development when this review was written is no longer in development, but this is still an excellent review ...


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@Chris's suggestion is very possible, high salt characteristically shows this towards the end of the gel. But there are additional suspects. This looks like it's just an agarose gel, Correct? I've seen a few things cause this including the gel not being level, the gel shifting during during it's run the percentage of agarose not being uniform and the ...


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Here is what the data says. UK government must have had some scientific evidence when it settled on a 10 variable-length sections of genome for their database, SGM+. In one such variable sections, some people have 10 repeats of CTTT, others have 11, others have 12 etc. The largest of those fragments, at its maximum length, are about 350 base pairs. The US ...


3

When designing PCR primers we typically use a minimum length of 20 bases, because the probability of a sequence of N bases appearing by random is $\frac{1}{4^N}$, and $\frac{1}{4^{20}}$ is about 9x$10^{-13}$, or about 1 in a trillion. Since the human genome is a little over 3 billion bases long, a 20 base sequence should appear only once. However, most of an ...


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With awk it is as simple as this (Assuming that the sequences are in fasta format and the sequences are not interrupted by line breaks): awk -v p=<some_patttern> '/>/{name=$0} !/>/{ s=$0 while (match(s,p)){ print name,substr(s, RSTART, RLENGTH) s=substr(s, RSTART+RLENGTH) } }' fastafile.fa This script will print all ...


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I'm no expert in MATLAB but I know that it is possible to do regular expressions in MATLAB with the general rules explained here. However there are alternative approaches and softwares you could use to achieve this with softwares that are freely available and quite powerful in performing such functions. Although I'm aware that perl and python are the ...



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