CHNOSZ (version 0.9-9)

util.seq: Functions to Work with Sequence Data

Description

Count amino acids in protein sequences, return one- or three-letter abbreviations of amino acids; count nucleotides in nucleic acid sequences, calculate DNA and RNA complements of nucleic acid sequences.

Usage

aminoacids(nchar=1, which=NULL)
  count.aa(seq)
  nucleicacids(seq, type = "DNA", comp = NULL, comp2 = NULL)

Arguments

nchar

numeric, $1$ to return one-letter, $3$ to return three-letter abbreviations for amino acids

which

character, which amino acids to name

seq

character, amino acid sequence of a protein (count.aa) or base sequence of a nucleic acid (nucleicacids)

type

character, type of nucleic acid sequence (DNA or RNA) (nucleicads)

comp

character, type of complement sequence

comp2

character, type of second complement sequence

Details

Depending on the value of nchar, aminoacids returns the one-letter abbreviations (1) or the three-letter abbreviations (3) or the names of the neutral amino acids ("") or the names of the amino acids with ionized side chains ("Z"). The default includes 20 amino acids in the order used in thermo$protein, unless which is provided, indicating the desired amino acids (either as 1- or 3-letter abbreviations or names of the neutral amino acids).

aminoacids takes a character value or list of character values containing a protein sequence. The number of occurrences of each type of amino acid is counted and output in a data frame with 20 columns, ordered in the same way as thermo$protein.

nucleicacids takes a DNA or RNA sequence and counts the numbers of bases of each type. Whether the sequence is DNA or RNA is specified by type. Setting comp to DNA or RNA tells the function to compute the base composition of that type of complement of the sequence. If comp2 is specified, another complement is taken. The two rounds of complementing can be used in a single function call e.g. to go from a sequence on DNA minus strand (given in seq) to the plus strand (with comp="DNA") and then from the DNA plus strand to RNA (with comp2="RNA"). The value returned by the function is a dataframe of base composition, which can be passed back to the function to obtain the overall chemical formula for the bases.

Examples

data(thermo)
## count amino acids in a sequence
count.aa("GGSGG")
# warnings are issued for unrecognized characters
suppressWarnings(atest <- count.aa("WhatAmIMadeOf?"))
# there are 3 "A" (alanine, the first amino acid alphabetically)
stopifnot(atest[,1]==3)

## count nucleobases in a sequence
nucleicacids("ACCGGGTTT")
# the DNA complement of that sequence
nucleicacids("ACCGGGTTT", comp="DNA")
# the RNA complement of the DNA complement
n <- nucleicacids("ACCGGGTTT", comp="DNA", comp2="RNA")
# the formula of the RNA complement
(nf <- nucleicacids(n, type="RNA"))
stopifnot(identical(nf, "C40H42N32O11"))