Exact(8)
The Vβ CDR3 sequences of expanded T-cell clones indicated a random usage of J segments in each of the expanded Vβ families.
Annotated smORFs display a lower than random usage of arginine, which is a hallmark of translated proteins (King and Jukes, 1969).
Nc (or ENC) is analogous to the effective number of alleles at a locus and ranges from 61 (random usage) to 20 (one codon per amino acid).
A high MI value means not random usage of the corresponding codon among genes that are expressed in the same tissue.
DOI: http://dx.doi.org/10.7554/eLife.03528.016 As a further indicator of smORF translation, we studied the amino acid composition of translated smORFs, compared to canonical long proteins and expected random usage.
Briefly, the RSCU of a codon (X) represents the number of times it appears in a sequence (observed usage), divided by the expected usage value, assuming random usage of synonymous codons for the corresponding amino acid (C).
Similar(52)
Genes display a non-random usage of synonymous codons and a measure of this non-randomness is RSCU (Relative synonymous codon usage).
In fact, RSS heterogeneity is a major reason for non-random usage in V(D J recombination.
Several authors have reported the non-random usage of specific dinucleotides and trinucleotides in plant genomes, and thus, the analysis of mutational bias should also take into account these compositional units.
We found that d s and the codon adaptation index (CAI) are in a negative correlation, therefore, we used a linear regression method to correct d s for bias caused by non-random usage of codons.
The Nc values, which range from 38 to 53, are all below the value of 61 that indicates random codon usage, so codon usage in all nine genomes is non-random.
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