
                               EMBOSS: findkm
     _________________________________________________________________
   
                                Program findkm
                                       
Function

   Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot
   
Description

   Takes a file of enzymatic data and plots Michaelis Menten and Hanes
   Woolf plots of the data. From these ot calculates the Michaelis Menten
   constant (Km) and the maximum velocity (Vmax) of the reaction.
   
Usage

   Here is a sample session with findkm.

%findkm
Calculates Km and Vmax for an enzyme reaction.
Enter name of file containing data: enztest.dat
Display on device [xwin]:

Command line arguments

   Mandatory qualifiers:
  [-infile]            infile     Enter name of file containing data
  [-outfile]           outfile    Output file name
   -graphlb            xygraph    Graph type

   Optional qualifiers: (none)
   Advanced qualifiers:
   -[no]plot           bool       S/V vs S

   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
   [-infile]
   (Parameter 1) Enter name of file containing data Input file Required
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.findkm
   -graphlb 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
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -[no]plot S/V vs S Yes/No Yes
   
Input file format

   The input file is a file of enzymatic data, [S] against V, Substrate
   concentration against reaction velocity.
   
   The data for the example run are shown below:

  0.10   2
  0.20   4
  0.50   9
  1.00  17
  2.00  29
  5.00  50
 10.00  67
 20.00  80
 50.00  91
100.00  95


Output file format

   Here is a sample output from the example above, together with the
   plots:

---Hanes Woolf Plot Calculations---
Slope of best fit line is a = 0.01
Coefficient in Eqn of line y = ma +b is b = 0.05
Where line cuts x axis = (-0.20, 0)
Where line cuts y axis = (0, 0.05)
Limit-point of graph for plot = (103.00, 1.08)

Vmax = 99.70, Km = 4.894612

   Click here for the graphical output
   
Data files

   See Input File Format
   
Notes

References

    1. Voet & Voet (1993) 'Biochemistry'
    2. Dawes 'Quantitative Problems in Biochemistry' 5th Edition.
    3. Manuel G. Claros, Francisco M. Canovas 'Lines&Kinetics: a graphic
       tool to deal with linear regressions and enzyme kinetics.'
       EMBnet.news vol 5.1
       http://www.uk.embnet.org/embnet.news/vol5_1/kinetics.html
    4. Cornish-Bowden (1996) 'Fundamentals of Enzyme kinetics' Portland
       Press, London.
       
Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

   Program name Description
   
Author(s)

   This application was written by Sinead O'Leary
   (soleary@hgmp.mrc.ac.uk)
   
   This application was modified for inclusion in EMBOSS by David Martin
   (david.martin@biotek.uio.no) at the Norwegian EMBnet node.
   
History

   Completed November 1999
   
   Modified May 2000
   
Target users

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