Functions to Work with Sequence Data

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Description

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

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Arguments

nchar

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

which

character, which amino acids to name

nucleic

data frame, counts of nucleic-acid bases

type

character, target type of nucleic acid (DNA or RNA)

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).

nucleic.formula returns a string representation of the chemical formula for each nucleic-acid composition contained in nucleic. The names of the bases are indicated by the column names of nucleic. At present, the formula is computed as the sum of the chemical formulas of the bases themselves, with no contribution from polymerization (dehydration) or phosphorylation.

nucleic.complement calculates the complement of the base composition given in nucleic. type specifies the type of nucleic acid of the complement - DNA (A, G, C, T) or RNA (A, G, C, U).

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

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## count nucleobases in a sequence
bases <- count.aa("ACCGGGTTT", type="DNA")
# the DNA complement of that sequence
DNA.comp <- nucleic.complement(bases)
# the RNA complement of the DNA complement
RNA.comp <- nucleic.complement(DNA.comp, type="RNA")
# the formula of the RNA complement (bases only)
nucleic.formula(RNA.comp)  # C40H42N32O11

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