Questions tagged [codon-usage]

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How large an expression boost is typical from codon optimization?

There are lots of different codon optimization approaches out there, and a lot of different qualitative reasons to want optimization (e.g., organism codon bias, GC content, avoiding secondary ...
jakebeal's user avatar
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1 vote
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computing relative synonymous codon usage from a coding sequence alignment while accounting for phylogenetic inertia?

I would like to compute the relative synonymous codon usage (RSCU) from coding sequence alignments. But since the coding sequences from an alignment are not independent realization, the statistics (...
SimonLL's user avatar
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Optimization of Signal Peptides

We are looking at modifying the signal peptide of a receptor in a common immortalized human cell line. The cell line already expresses an unusually high amount of the protein, but much of it is not ...
Atl LED's user avatar
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5 votes
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How many possible codons?

Consider a codon of the form NNK (where N = Adenine, Cytosine, Guanine or Uracil & K = Uracil or Guanine). How many codons are now available? I know if all were available there would be 4^3 = 64 ...
O.kth's user avatar
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3 votes
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Codon tables and the wobble hypothesis

In E. coli, there are only 47 different tRNAs but 61 potential anticodons. This is because, from what I understand, the third base of the anticodon can pair by wobble rules. However, it is known that ...
bravetang8's user avatar
10 votes
3 answers

Why does Nature use a 4-level system to encode information in DNA?

First, I am not a biologist, so this question might be naive: Computer information processing and storage is based on 2-digit system of bits with values 0 and 1. Now, DNA stores the information in a ...
Mario Krenn's user avatar
3 votes
4 answers

Why are there both stop and start codons?

Based on my understanding from wikipedia, there is the (RNA) start codon AUG and the stop codons UAA, UGA, UAG. AUG can also encode Methionine, I'm assuming if it appears in the middle of a mRNA ...
Yehosef's user avatar
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6 votes
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Whole genome amino acid composition tool?

I'm interested in a statistical tool to get bacterial codon usage at genomic level. Ideally, the tool should be flexible to analyse hundreds of bacterial genomes. I've looked in MeSH terms database ...
biotech's user avatar
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5 votes
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How are the various classes of E coli genes determined?

Looking at some more detailed codon usage tables, genes may be further clustered into three gene classes: Metabolic genes, highly expressed genes during exponential growth, and horizontal gene ...
bobthejoe's user avatar
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11 votes
3 answers

DNA synthesis companies: cost per base, turn-around time, codon-optimization algorithms

I would like to synthesize a 3.4kb gene (originally isolated from soil bacteria) and transform it into E. coli. There are several companies (DNA2.0, GeneScript, BlueHeron) which will synthesize the ...
Gergana Vandova's user avatar