R: To Compute the Theoretical Isoelectric Point

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. 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.

### 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

    #
    # 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

[Package seqinr version 3.4-5 Index]