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<!--  $Id: Interval_Mapping.html,v 1.4 1999/04/29 16:16:49 fw Exp $  -->
<head>
<title>Interval_Mapping</title>
</head>

<BODY BGCOLOR=#ffffff>

<h2>Interval_Mapping</h2>

This program tries to compute a genetic map using deficiency data.<p>

<h3>Menu items:</h3>

<ul>

<li><strong>Quit</strong>: quits the window.<p>

<li><strong>Help</strong>: brings up this help.<p>

<li><strong>Print</strong>: prepares a Post Script file in
./PS which you can then print on your local laser printer.<p>

<li><strong>Parse database</strong>: Must be run once, when you have
changed the 2_point_data It looks for deficiency data and reorgaizes
them internally for later use by this package. In particular, genes
and def are sorted into contigs defined as a set of genes and
deficiencies tested against each other.<p>

<li><strong>Read file</strong>: This allows you to run the same
analysis on some data that you do not want to parse into your
database.  The data file should consist of ND+1 lines of NM symbols 1
or 0 where NM is the number of markers and ND the number of
deficiencies. A 1 indicates that the deficiency uncovers the gene.
The first line indicates which genes to take into account.  It should
have NM 1 to use everything, any 0 will discard the corresponding
column. i.e. gene from the analysis.  One can also impose the order of
subgroups and block some genes together. An example input file is
given in the next help page.<p>

<li><strong>Get contig</strong>: Ask for a contig number. If you give
a bad answer, it does not matter. The number of contigs is specified
when you Parse the database.<p>

<li><strong>Cost</strong>: Gives the cost of the running order of the
marker, The cost function is n for a deficiency splitted in n+1
discontinuous pieces There is also a way to impose the order of some
of the markers, but I this is not yet done in a smooth way.<p>

<li><strong>Shuffle</strong>: Reshuffles the markers before a new try.<p>

<li><strong>Monte Carlo</strong>: Inserts the markers one by one in an
expanding list. It tries to keep the cost to a minimum and remembers n
previous configurations, n is a parameter asked from the user. We had
fast and good results with NM = ND = about 20 and n = 5 This is a
monte carlo, so you must repeat the search several times.  Once a good
solution is found, it will no longer print the bad ones.  With NM = ND
around 100, n = 8, it was very slow but the results were rather good.<p>

<li><strong>Intrinsic tree</strong>: This is an independant fast and
innacurate algorithm to reorder the genes. It should be completed by
the next button:<p>

<li><strong>Refine tree</strong>: This should better the results of
the preceding button but is not yet available.<p>

<li><strong>Map</strong>: Creates a new window with a useful graphic
presentation of the data. It is interesting even on the standard data,
before selecting the order option. The Map graph has its own menu with
the usual options Quit-Help-Print. The Help is the same one. Quit
quits the application. Print prepares defmapxxx.PS.  With NM = ND =
100, the resulting graph will not be printed on my laser, probably it
is a font problem, sorry.<p>

<li><strong>Histo</strong>: Plots the marginal ditributions :
Histogram of the number of deficiencies carrying a given number of
markers and vice versa

</ul>

to <a href="TOC.html">Table of Contents</a><p>
</pre>

last edited: July 1994<p>

</BODY>