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findkm.html
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<HTML>
<HEAD>
<TITLE>
EMBOSS: findkm
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
findkm
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Find Km and Vmax for an enzyme reaction
<H2>
Description
</H2>
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.
<H2>
Usage
</H2>
<b>Here is a sample session with findkm</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>findkm -graph cps </b>
Find Km and Vmax for an enzyme reaction
Enzyme kinetics data (application-specific) file: <b>enztest.dat</b>
Output file [enztest.findkm]: <b></b>
Created findkm.ps
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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,
tekt, tek, 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 standard output
-filter boolean Read standard input, write 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. 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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-infile]<br>(Parameter 1)</td>
<td>Enzyme kinetics data (application-specific) file</td>
<td>Input file</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.findkm</td>
</tr>
<tr>
<td>-graphlb</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-[no]plot</td>
<td>S/V vs S</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
</table>
<H2>
Input file format
</H2>
The input file is a file of enzymatic data, [S] against V, Substrate
concentration against reaction velocity.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: enztest.dat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: enztest.findkm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
---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 = 4.894611
</pre>
</td></tr></table><p>
<p><h3>Graphics File: findkm.ps</h3>
<p><img src="findkm.1.findkm.gif" alt="[findkm results]">
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ol>
<li>
Voet & Voet (1993) 'Biochemistry'
<li>
Dawes 'Quantitative Problems in Biochemistry' 5th Edition.
<li>
Manuel G. Claros, Francisco M. Canovas
'Lines&Kinetics: a graphic tool to deal with linear regressions and
enzyme kinetics.'
EMBnet.news vol 5.1
<a href="http://www.uk.embnet.org/embnet.news/vol5_1/kinetics.html">
http://www.uk.embnet.org/embnet.news/vol5_1/kinetics.html</a>
<li>
Cornish-Bowden (1996) 'Fundamentals of Enzyme kinetics'
Portland Press, London.
</ol>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It exits with a status of 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
</table>
<H2>
Author(s)
</H2>
Sinead O'Leary (current e-mail address unknown)
<br>
while she was at:
<br>
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK
<p>
This application was modified by
David Martin (dmartin © rfcgr.mrc.ac.uk)
<br>
<H2>
History
</H2>
Completed November 1999
<p>
Modified May 2000
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>