
                                EMBOSS: iep
     _________________________________________________________________
   
                                  Program iep
                                       
Function

   Calculates the isoelectric point of a protein
   
Description

   This calculates the isoelectric point of a protein from its amino acid
   composition assuming that no electrostatic interactions change the
   propensity for ionization.
   
   Adjusting the pH of an aqueous protein solution to the point where the
   numbers of positive and negative charges on the protein are equal
   brings the protein to its isoelectric point. This is often the point
   of lowest solubility, presumably because it is the point at which
   there are fewest intermolecular repulsions, so that the molecules tend
   to form aggregates.
   
   The application can make a plot of the ionization curve with respect
   to pH and can write an output file of the data.
   
Usage

   Here is a sample session with iep.

% iep sw:laci_ecoli
Output file [laci_ecoli.iep]:

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequencea]         seqall     Sequence database USA
*  -graph              xygraph    Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -step               float      pH step value
   -amino              integer    Number of N-termini
   -[no]termini        bool       Include charge at N and C terminus
   -plot               bool       Plot charge vs pH
   -[no]report         bool       Write results to a file

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequencea]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   -outfile Output file name Output file <sequence>.iep
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -step pH step value Number from 0.010 to 1.000 .5
   -amino Number of N-termini Any integer value 1
   -[no]termini Include charge at N and C terminus Yes/No Yes
   -plot Plot charge vs pH Yes/No No
   -[no]report Write results to a file Yes/No Yes
   
Input file format

   Any protein sequence USA.
   
Output file format

   This is the output file from the example:
   For each pH point it gives the number of bound electrons and the
   charge.
     _________________________________________________________________
   
IEP of LACI_ECOLI from 1 to 360
Isoelectric Point = 6.8820

   pH     Bound    Charge
  1.00    81.96    37.96
  1.50    81.89    37.89
  2.00    81.65    37.65
  2.50    80.91    36.91
  3.00    78.79    34.79
  3.50    73.70    29.70
  4.00    65.15    21.15
  4.50    56.73    12.73
  5.00    51.75     7.75
  5.50    49.36     5.36
  6.00    47.63     3.63
  6.50    45.56     1.56
  7.00    43.59    -0.41
  7.50    42.27    -1.73
  8.00    41.22    -2.78
  8.50    39.87    -4.13
  9.00    38.26    -5.74
  9.50    36.24    -7.76
 10.00    33.03   -10.97
 10.50    28.46   -15.54
 11.00    23.58   -20.42
 11.50    19.41   -24.59
 12.00    15.19   -28.81
 12.50     9.75   -34.25
 13.00     4.64   -39.36
 13.50     1.75   -42.25
 14.00     0.59   -43.41
     _________________________________________________________________
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   0 if successful.
   
Known bugs

   None.
   
See also

   Program name Description
   backtranseq Back translate a protein sequence
   charge Protein charge plot
   checktrans Reports STOP codons and ORF statistics of a protein
   sequence
   compseq Counts the composition of dimer/trimer/etc words in a sequence
   emowse Protein identification by mass spectrometry
   freak Residue/base frequency table or plot
   mwfilter Filter noisy molwts from mass spec output
   octanol Displays protein hydropathy
   pepinfo Plots simple amino acid properties in parallel
   pepstats Protein statistics
   pepwindow Displays protein hydropathy
   pepwindowall Displays protein hydropathy of a set of sequences
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Completed 1st August 1999.
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
