ucoweight: Weight of each synonymous codon

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/synonymous.R

Description

Returns a list containing, for each of the 20 amino acids + STOP codon, the codon usage bias of each of the synonymous codon according to a given codon sequence.

Usage

1
ucoweight(sequence, numcode = 1)

Arguments

sequence

A nucleic acids sequence

numcode

The genetic code number as in translate

Value

a list containing, for each of the 20 amino acids and STOP codon (list tags), the weight of each synonymous codon (including the original one).

Author(s)

L. Palmeira

References

citation("seqinr")

See Also

synsequence

Examples

1
2

Example output

$F

ttt ttc 
  3   4 

$L

tta ttg ctt ctc cta ctg 
  1   2   3   3   1  13 

$S

tct tcc tca tcg agt agc 
  1   3   2   2   4   2 

$Y

tat tac 
  2   2 

$`*`

taa tag tga 
  0   0   1 

$C

tgt tgc 
  1   1 

$W
tgg 
  0 

$P

cct ccc cca ccg 
  0   1   1   6 

$H

cat cac 
  7   3 

$Q

caa cag 
  2   7 

$R

cgt cgc cga cgg aga agg 
  4   7   1   1   0   0 

$I

att atc ata 
  6   9   0 

$M
atg 
  8 

$T

act acc aca acg 
  1   8   2   8 

$N

aat aac 
  4   5 

$K

aaa aag 
  9   2 

$V

gtt gtc gta gtg 
  4   5   0   9 

$A

gct gcc gca gcg 
  5   6   1   7 

$D

gat gac 
  9   3 

$E

gaa gag 
 12   1 

$G

ggt ggc gga ggg 
  4   3   2   0 

seqinr documentation built on Aug. 13, 2017, 3:01 a.m.