findkm |
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Function
Calculate and plot enzyme reaction dataDescription
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 |
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, pdf, svg | 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
Data files
None.Notes
None.References
- Voet & Voet (1993) 'Biochemistry'
- Dawes 'Quantitative Problems in Biochemistry' 5th Edition.
- 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
- 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 |
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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 © 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 © emboss.open-bio.org) not to the original author.
History
Completed November 1999Modified May 2000