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Calculate and plot enzyme reaction data


findkm reads a file of enzymatic reaction data (substrate concentration [S] versus reaction velocity [V]) and draws Michaelis Menten and Hanes Woolf plots of the data. From these it calculates the Michaelis Menten constant (Km) and the maximum velocity (Vmax) of the reaction. An output file with all relevant data is written.


Here is a sample session with findkm

% findkm -graph cps 
Calculate and plot enzyme reaction data
Enzyme kinetics data (application-specific) file: enztest.dat
Output file [enztest.findkm]: 


Go to the input files for this example
Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infile]            infile     Enzyme kinetics data (application-specific)
  [-outfile]           outfile    [*.findkm] Output file name
   -graphlb            xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, das, xterm, png, gif)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -[no]plot           boolean    [Y] S/V vs S

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-graphlb" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers Allowed values Default
(Parameter 1)
Enzyme kinetics data (application-specific) file Input file Required
(Parameter 2)
Output file name Output file <*>.findkm
-graphlb Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, das, xterm, png, gif EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers Allowed values Default
Advanced (Unprompted) qualifiers Allowed values Default
-[no]plot S/V vs S Boolean value Yes/No Yes

Input file format

The input file is a file of enzymatic data, [S] against V, Substrate concentration against reaction velocity.

Input files for usage example

File: enztest.dat

  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

Output files for usage example

File: enztest.findkm

---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

Graphics File:

[findkm results]

Data files





  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.' vol 5.1
  4. Cornish-Bowden (1996) 'Fundamentals of Enzyme kinetics' Portland Press, London.



Diagnostic Error Messages


Exit status

It exits with a status of 0.

Known bugs


See also

Program name Description


Sinead O'Leary (current e-mail address unknown)
while she was at:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

This application was modified by David Martin (dmartin ©


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.