findkm

 

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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:6.2.0

   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)

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)
infile Enzyme kinetics data (application-specific) file Input file Required
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.findkm
-graphlb xygraph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-[no]plot boolean S/V vs S Boolean value Yes/No Yes
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
"-graphlb" associated xygraph qualifiers
-gprompt boolean Graph prompting Boolean value Yes/No N
-gdesc string Graph description Any string  
-gtitle string Graph title Any string  
-gsubtitle string Graph subtitle Any string  
-gxtitle string Graph x axis title Any string  
-gytitle string Graph y axis title Any string  
-goutfile string Output file for non interactive displays Any string  
-gdirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 (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 © rfcgr.mrc.ac.uk)

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