computePI {seqinr}R Documentation

To Compute the Theoretical Isoelectric Point

Description

This function calculates the theoretical isoelectric point of a protein. Isoelectric point is the pH at which the protein has a neutral charge. These estimate does not account for the post-translational modifications.

Usage

computePI(seq)

Arguments

seq AA sequence as a vector of chars

Value

It returns the pI.

Note

Protein pI is calculated using pK values of amino acids described in Bjellqvist et al. See also SEQINR.UTIL for more details.

Author(s)

D. Charif

References

The algorithm is quite the same as the one which is implemented at the following url: http://www.expasy.org/tools/pi_tool-doc.html To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.

See Also

SEQINR.UTIL

Examples

ss = read.fasta(File=system.file("sequences/seqAA.fasta",package = "seqinr"),seqtype="AA")
computePI(ss[[1]]) 

[Package seqinr version 1.0-2 Index]