findkm



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Calculate and plot enzyme reaction data

Description

   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.

Usage

   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]:

Created findkm.ps


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

Command line arguments

Calculate and plot enzyme reaction data
Version: EMBOSS:6.4.0.0

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

   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 and exit. 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
   -version            boolean    Report version number and exit


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.ps

   [findkm results]

Data files

   None.

Notes

   None.

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

   None.

Diagnostic Error Messages

   None.

Exit status

   It exits with a status of 0.

Known bugs

   None.

See also

   Program name     Description

Author(s)

   Sinead O'Leary formerly at:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

   This application was modified by David Martin

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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

   None