seqinr (version 3.4-5)

computePI: 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. This estimate does not account for the post-translational modifications.

Usage

computePI(seq)

Arguments

seq

Protein sequence as a vector of single chars in upper case

Value

The theoretical isoelectric point (pI) as a numerical vector of length one.

References

The algorithm is the same as the one which is implemented at the following url: http://www.expasy.org/tools/pi_tool-doc.html but with many trials in case of convergence failure of the non-linear regression procedure. citation("seqinr")

See Also

SEQINR.UTIL

Examples

# NOT RUN {
#
# Simple sanity check with all 20 amino-acids in one-letter code alphabetical order:
#
prot <- s2c("ACDEFGHIKLMNPQRSTVWY")
stopifnot(all.equal(computePI(prot), 6.78454))
#
# Read a protein sequence in a FASTA file and then compute its pI :
#
myProts <- read.fasta(file = system.file("sequences/seqAA.fasta",
 package = "seqinr"), seqtype = "AA")
computePI(myProts[[1]]) # Should be 8.534902
# }