To Compute the Theoretical Isoelectric Point

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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

1

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.

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, J.R. Lobry

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

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#
# 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

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