Author image Alexandre Masselot
and 1 contributors

NAME

  computePI.pl - Compute isoelectric point (pI)

SYNOPSIS

./computePI.pl [--method=METHOD] [--current=CURRENT] [--saveparam=PARAM] | [--readparam=PARAM] [--calibratefrom=CAL] [--settings=SETTINGS] [--out=OUT] (filein1 [ filein2[...]] | - )

OPTIONS

--method

Algorithm : iterative (default) or Patrickios (approximated).

--current

Coefficients used for the iterative algorithm. Currently available are: Lehninger (default), EMBOSS, Rodwell, Sillero, Solomon.

--out

Output text file (or STDOUT if no such argument is given)

--calibratefrom

Calibrate the algorithm by fitting some experimental data. File format of blank-separated columns: "amino acid sequences" "isoelectric point" "additional cols" ...

--saveparam

Save current params in PARAM, including calibration.

--readparam

Retrieve current params in PARAM, including calibration.

--settings

XML file with user-supplied additional coefficients. See 'piset.dtd'.

--help

Print a brief help message and exits.

--man

Print the manual page and exits.

All remaining arguments are names of input files; or '-' for the standard input.

DESCRIPTION

This program will estimate the isoelectric point (pI) for a given list of peptides. The point is computed by an iterative algorithm or by a theoretical approximation using the regressed dissociation constants (Patrickios et al, Anal. BioChem. 231, 82-91, 1995).