seqinr: AAstat – R documentation

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AAstat

To Get Some Protein Statistics

Description

Returns simple protein sequence information including the number of residues, the percentage physico-chemical classes and the theoretical isoelectric point. The functions ignore ambiguous amino acids (e.g. "B", "Z", "X", "J").

Usage

AAstat(seq, plot = TRUE)

Arguments

`seq`	a protein sequence as a vector of upper-case chars
`plot`	if `TRUE`, plots the presence of residues splited by physico-chemical classes along the sequence.

Value

A list with the three following components:

`Compo`	A factor giving the amino acid counts.
`Prop`	A list giving the percentage of each physico-chemical classes (Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar, Charged, Positive, Negative).
`Pi`	The theoretical isoelectric point

Author(s)

D. Charif, J.R. Lobry

References

citation("seqinr")

Examples

seqAA <- read.fasta(file = system.file("sequences/seqAA.fasta", package = "seqinr"),
   seqtype = "AA")
  AAstat(seqAA[[1]])

seqinr

Biological Sequences Retrieval and Analysis

v4.2-16

GPL (>= 2)

Authors

Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

Initial release

2022-05-19