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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:6.6.0.0
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
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