ComputeGC12syn: GC content 1st and 2nd position of synonymous codons

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

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.