util.seq: Functions to Work with Sequence Data

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

Functions to Work with Sequence Data

Description

Return names or one- or three-letter abbreviations of amino acids.

Usage

  aminoacids(nchar = 1, which = 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

Details

aminoacids returns the one-letter abbreviations (nchar=‘⁠1⁠’) or the three-letter abbreviations (nchar=‘⁠3⁠’) or the names of the neutral amino acids (nchar=‘⁠""⁠’) or the names of the amino acids with ionized side chains (nchar=‘⁠"Z"⁠’). The output includes 20 amino acids in alphabetic order by 1-letter abbreviation (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).

See Also

count.aa for counting amino acids or nucleic-acid bases in a sequence; protein.formula for calculating the chemical formulas of proteins.

Examples

## Count nucleobases in a sequence
bases <- count.aa("ACCGGGTTT", type = "DNA")

CHNOSZ documentation built on May 29, 2024, 3:30 a.m.