| findkm

## Function

Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot

## Description

Takes a file of enzymatic data and plots 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.

## Usage

Here is a sample session with findkm

    % findkm -graph cps
    Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot
    Enter name of file containing data: ../../data/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

       Mandatory qualifiers:
      [-infile]            infile     Enter name of file containing data
      [-outfile]           outfile    Output file name
       -graphlb            xygraph    Graph type

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

       Associated qualifiers:
      "-outfile" related qualifiers
       -odirectory2         string     Output directory
      "-graphlb" related qualifiers
       -gprompt             boolean    Graph prompting
       -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 standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | Enter name of file containing data | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.findkm
-graphlb | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11
Optional qualifiers | Allowed values | Default
(none)
Advanced 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: ../../data/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

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)

This application was written by 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 © hgmp.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