ComputeGC12syn: GC content 1st and 2nd position of synonymous codons
In fredysiegrist/statanacoseq: Statistical Analyses of Codon Usage in Custom Genome Sequences
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
ComputeGC3syn Computes the G+C content at the 1st and 2nd position of synonymous codons
Usage
1
ComputeGC12syn(tD)
Arguments
tD
Nucleotide character string
Details
Computes the GC content of the 1st and 2nd position of synonymous codons to estimate the background
GC content when compared with the GC content at the 3rd position. By definition, GC12s values are
the proportion of GC nucleotides at the fixed first and less variable second coding position of
synonymous codons. This can be used to evaluate the degree of base composition bias.
Value
vector of (o/n)first (o/n)second
Author(s)
Siegrist, F. and Cannarozzi, G. M. gina@cannarozzi.com
See Also
seqinr statanacoseq ComputeGC3syn
Examples
1
2
ComputeGC12syn('ATGTGGTACTCCGACTACGGAGGATAA')
plot(mean(ComputeGC12syn(toupper(c2s(mylist(whatout=1)[[1]])))), ComputeGC3syn(toupper(c2s(mylist(whatout=1)[[1]]))))
fredysiegrist/statanacoseq documentation built on May 16, 2019, 2:44 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
ComputeGC3syn Computes the G+C content at the 1st and 2nd position of synonymous codons
Usage
1 | ComputeGC12syn(tD)
|
Arguments
tD |
Nucleotide character string |
Details
Computes the GC content of the 1st and 2nd position of synonymous codons to estimate the background GC content when compared with the GC content at the 3rd position. By definition, GC12s values are the proportion of GC nucleotides at the fixed first and less variable second coding position of synonymous codons. This can be used to evaluate the degree of base composition bias.
Value
vector of (o/n)first (o/n)second
Author(s)
Siegrist, F. and Cannarozzi, G. M. gina@cannarozzi.com
See Also
seqinr statanacoseq ComputeGC3syn
Examples
1 2 | ComputeGC12syn('ATGTGGTACTCCGACTACGGAGGATAA')
plot(mean(ComputeGC12syn(toupper(c2s(mylist(whatout=1)[[1]])))), ComputeGC3syn(toupper(c2s(mylist(whatout=1)[[1]]))))
|
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