## File: computePI.Rd

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r-cran-seqinr 3.4-5-2
 1234567891011121314151617181920212223242526272829303132333435363738394041 \name{computePI} \alias{computePI} \title{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{ \item{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: \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. \code{citation("seqinr")} } \author{D. Charif, J.R. Lobry} \note{ Protein pI is calculated using pK values of amino acids described in Bjellqvist et al. See also \code{SEQINR.UTIL} for more details. } \seealso{\code{\link{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 } \keyword{manip}