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<?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>tmhmm</name>
<version>2.0C</version>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/cbs_package.xml"/>
<doc>
<title>tmhmm</title>
<description>
<text lang="en">prediction of transmembrane helices in proteins.</text>
</description>
<sourcelink>http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm</sourcelink>
<reference>
</reference>
<reference>
</reference>
<doclink>http://www.cbs.dtu.dk/services/TMHMM//</doclink>
</doc>
<category>sequence:protein:2D_structure</category>
<category>structure:2D_structure</category>
</head>
<parameters>
<parameter ishidden="1" iscommand="1">
<name>tmhmm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"tmhmm "</code>
<code proglang="python">"tmhmm "</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>sequence</name>
<prompt lang="en">Input Sequence</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" $value "</code>
<code proglang="python">" " + str( value )</code>
</format>
<argpos>50</argpos>
</parameter>
<parameter >
<name>output_opt</name>
<prompt lang="en">output options</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<flist>
<felem>
<value>0</value>
<label>Extensive, with graphics</label>
<code proglang="perl">" -noshort "</code>
<code proglang="python">" -noshort "</code>
</felem>
<felem>
<value>1</value>
<label>Extensive, no graphics</label>
<code proglang="perl">" -noplot "</code>
<code proglang="python">" -noplot "</code>
</felem>
<felem>
<value>2</value>
<label>One line per protein, no graphics</label>
<code proglang="perl">" -short "</code>
<code proglang="python">" -short "</code>
</felem>
</flist>
<argpos>10</argpos>
</parameter>
<parameter>
<name>v1</name>
<prompt lang="en">Use old model (version 1).</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -v1 ": ""</code>
<code proglang="python">( ""," -v1 ")[ bool( value ) ]</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter isstdout="1">
<name>results</name>
<prompt lang="en">tmhmm report.</prompt>
<type>
<datatype>
<superclass>Report</superclass>
<class>tmhmm</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"tmhmm.out"</code>
<code proglang="python">"tmhmm.out"</code>
</filenames>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<p><strong>Long output format</strong></p>
<p>The first few lines gives some statistics:</p>
<ul>
<li>Length: the length of the protein sequence.</li>
<li>Number of predicted TMHs: The number of predicted transmembrane helices.</li>
<li>Exp number of AAs in TMHs: The expected number of amino acids intransmembrane
helices. If this number is larger than 18 it is very likely to be a transmembrane
protein (OR have a signal peptide).</li>
<li>Exp number, first 60 AAs: The expected number of amino acids in transmembrane
helices in the first 60 amino acids of the protein. If this number more
than a few, you should be warned that a predicted transmembrane helix in
the N-term could be a signal peptide.</li>
<li>Total prob of N-in: The total probability that the N-term is on the cytoplasmic
side of the membrane.</li>
<li>POSSIBLE N-term signal sequence: a warning that is produced when "Exp number,
first 60 AAs" is larger than 10.</li>
</ul>
<p><strong>Short output format</strong></p>
<p>In the short output format one line is produced for each protein with no
graphics. Each line starts with the sequence identifier and then these
fields:</p>
<ul>
<li>"len=": the length of the protein sequence.</li>
<li>"ExpAA=": The expected number of amino acids intransmembrane helices (see
above).</li>
<li><tt>"First60="</tt>: The expected number of amino acids in transmembrane
helices in the first 60 amino acids of the protein (see above).</li>
<li><tt>"PredHel=": </tt>The number of predicted transmembrane helices by N-best.</li>
<li>"Topology=": The topology predicted by N-best.</li>
</ul>
<p>For the example above the short output would be (except that it would be
on one line):</p>
<p>
<tt>COX2_BACSU</tt><br />
<tt>len=278</tt><br />
<tt>ExpAA=68.69</tt><br />
<tt>First60=39.89</tt><br />
<tt>PredHel=3</tt><br />
<tt>Topology=i7-29o44-66i87-109o</tt>
</p>
<p>The topology is given as the position of the transmembrane helices separated
by 'i' if the loop is on the inside or 'o' if it is on the outside. The
above example '<tt>i7-29o44-66i87-109o' means that it starts on the inside,
has a predicted TMH at position 7 to 29, the outside, then a TMH at position
44-66 etc.</tt>
</p>
</div>
</comment>
</parameter>
<parameter isout="1">
<name>eps</name>
<prompt lang="en">Plot of probabilities</prompt>
<type>
<datatype>
<superclass>Binary</superclass>
<class>tmhmm_graphic</class>
</datatype>
<dataFormat>EPS</dataFormat>
</type>
<precond>
<code proglang="perl">output_opt == "0"</code>
<code proglang="python">output_opt == "0"</code>
</precond>
<filenames>
<code proglang="perl">"*.eps"</code>
<code proglang="python">"*.eps"</code>
</filenames>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<p>The plot shows the posterior probabilities
of inside/outside/TM helix. Here one can see possible weak TM helices that
were not predicted, and one can get an idea of the certainty of each
segment in the prediction.</p>
<p>At the top of the plot (between 1 and 1.2) the N-best prediction is shown.</p>
<p>The plot is obtained by calculating the total probability that a
residue sits in helix, inside, or outside summed over all possible
paths through the model. Sometimes it seems like the plot and the
prediction are contradictory, but that is because the plot shows probabilities
for each residue, whereas the prediction is the over-all most probable
structure. Therefore the plot should be seen as a complementary source
of information.</p>
</div>
</comment>
</parameter>
<parameter isout="1">
<name>png</name>
<prompt lang="en">tmhmm graphic.</prompt>
<type>
<datatype>
<superclass>Binary</superclass>
<class>tmhmm_graphic</class>
</datatype>
<dataFormat>png</dataFormat>
</type>
<precond>
<code proglang="perl">output_opt == "0"</code>
<code proglang="python">output_opt == "0"</code>
</precond>
<filenames>
<code proglang="perl">"*.png"</code>
<code proglang="python">"*.png"</code>
</filenames>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<p>The plot shows the posterior probabilities
of inside/outside/TM helix. Here one can see possible weak TM helices that
were not predicted, and one can get an idea of the certainty of each
segment in the prediction.</p>
<p>At the top of the plot (between 1 and 1.2) the N-best prediction is shown.</p>
<p>The plot is obtained by calculating the total probability that a
residue sits in helix, inside, or outside summed over all possible
paths through the model. Sometimes it seems like the plot and the
prediction are contradictory, but that is because the plot shows probabilities
for each residue, whereas the prediction is the over-all most probable
structure. Therefore the plot should be seen as a complementary source
of information.</p>
</div>
</comment>
</parameter>
</parameters>
</program>
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