/var/lib/mobyle/programs/predator.xml is in mobyle-programs 5.1.1-1.
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<!-- 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>predator</name>
<version>2.1.2</version>
<doc>
<title>PREDATOR</title>
<description>
<text lang="en">Protein secondary structure prediction from a single sequence or a set of sequences</text>
</description>
<authors>D. Frishman & P. Argos</authors>
<reference>Frishman, D. and Argos, P. (1996) Incorporation of long-distance interactions into a secondary structure prediction algorithm. Protein Engineering, 9, 133-142.</reference>
<reference>Frishman, D. and Argos, P. (1997) 75% accuracy in protein secondary structure prediction. Proteins, 27, 329-335.</reference>
<reference>Frishman,D and Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins: structure, function and genetics, 23, 566-579.</reference>
<reference>Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22: 2577-2637.</reference>
<sourcelink>ftp://ftp.ebi.ac.uk/pub/software/unix/predator/</sourcelink>
</doc>
<category>sequence:protein:2D_structure</category>
<category>structure:2D_structure</category>
<command>predator</command>
</head>
<parameters>
<paragraph>
<name>inputfile</name>
<prompt>Input file</prompt>
<comment>
<text lang="en">You must enter either a protein sequences or alignment file</text>
</comment>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>sequences</name>
<prompt lang="en">Protein sequence(s) File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>1,n</card>
</type>
<precond>
<code proglang="perl">defined $sequences and not defined $alignment</code>
<code proglang="python">sequences is not None and alignment is None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " $value" : ""</code>
<code proglang="python">("" , " " + str(value) )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">You must fill either sequences or alignment not both</text>
</message>
<code proglang="perl">not defined $alignment</code>
<code proglang="python">alignment is None</code>
</ctrl>
<argpos>100</argpos>
</parameter>
<parameter issimple="1">
<name>alignment</name>
<prompt lang="en">Protein Alignment File</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<dataFormat>CLUSTAL</dataFormat>
<dataFormat>MSF</dataFormat>
</type>
<precond>
<code proglang="perl">defined $alignment and not defined $sequences</code>
<code proglang="python">alignment is not None and sequences is None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " $value" : ""</code>
<code proglang="python">("" , " " + str(value))[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">You must fill either alignment or sequences not both</text>
</message>
<code proglang="perl">not defined sequences</code>
<code proglang="python">sequences is None</code>
</ctrl>
<argpos>101</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>prediction</name>
<prompt lang="en">Prediction options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>single</name>
<prompt lang="en">Perform single sequence prediction. Ignore other sequences in the set for computing the prediction (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $all </code>
<code proglang="python">not all </code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -s" : ""</code>
<code proglang="python">( "" , " -s" )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>dont_copy</name>
<prompt lang="en">Do not copy assignment directly from the PDB database (-u)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -u" : ""</code>
<code proglang="python">( "" , " -u" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Do not copy assignment directly from the PDB database if query sequence is found in PDB. By default, the known conformation of 7-residue segments will be used if they are identical to a 7-residue fragment in the query sequence.</text>
</comment>
</parameter>
<parameter>
<name>dssp</name>
<prompt lang="en">Use DSSP target assignment (-d)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $dssp_file</code>
<code proglang="python">dssp_file is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -d" : ""</code>
<code proglang="python">( "" , " -d" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Use DSSP target assignment (default is STRIDE). The predictions made with DSSP and STRIDE target assignments are optimized to reproduce these assignments as well as possible.</text>
</comment>
</parameter>
<parameter>
<name>percentid</name>
<prompt lang="en">Find a subset of sequences with no more than this identity between any pair of sequences (-n)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -n$value" : ""</code>
<code proglang="python">( "" , " -n" + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>input</name>
<prompt lang="en">Input parameters</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>all</name>
<prompt lang="en">Make prediction for All sequences in the input file (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $seqid</code>
<code proglang="python">seqid is None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a" : ""</code>
<code proglang="python">( "" , " -a" )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>seqid</name>
<prompt lang="en">Make prediction for this sequence (give its id) (-i)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -i$value" : ""</code>
<code proglang="python">( "" , " -i" + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">This option is case sensitive!</text>
</comment>
</parameter>
<parameter>
<name>stride_file</name>
<prompt lang="en">STRIDE file (-x)</prompt>
<type>
<datatype>
<class>StrideReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -x$value" : ""</code>
<code proglang="python">( "" , " -x" + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>dssp_file</name>
<prompt lang="en">DSSP file (-y)</prompt>
<type>
<datatype>
<class>DsspOutput</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -y$value" : ""</code>
<code proglang="python">( "" , " -y"+str( value ) )[ value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter ismandatory="1">
<name>pdb_chain</name>
<prompt lang="en">PDB Chain (-z)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $dssp_file or defined $stride_file</code>
<code proglang="python">dssp_file is not None or stride_file is not None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -z$value" : " -z-"</code>
<code proglang="python">( " -z-" , " -z" + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output parameters</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>long</name>
<prompt lang="en">Long output form (-l)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -l" : ""</code>
<code proglang="python">( "" , " -l" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Every output line contains residue number, three-letter residue name, one-letter residue name, predicted secondary structural state and reliability estimate. If a STRIDE or DSSP secondary structure assignment has been read (see other options), the known assignment will also be shown in the output for comparison. By default the short output form is used.</text>
</comment>
</parameter>
<parameter>
<name>other_info</name>
<prompt lang="en">Output other additional information if available (-h)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -h" : ""</code>
<code proglang="python">( "" , " -h" )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter isstdout="1">
<name>predator_output</name>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<comment>
<text lang="en">
Short output form:
</text>
<text lang="en">
Secondary structure states of amino acids are indicated by the letters
"H" (helix), "E" (extended or sheet), and "_" (coil).</text>
<text lang="en">
Long output form ( option -L selected ):
</text>
<text lang="en">
Secondary structure states of amino acids are indicated by letters "H"
or "h" (helix), "E" or "e" (extended), and "C" or "c" (coil). The
prediction is shown in lower case except for those residues for which
the assignment was directly copied from the PDB database. This feature
is added so that you can distinguish between the predictions actually
made by PREDATOR and those taken from known structures.
The prediction is contained in the records beginning with the
identifier PRED in the first columns. For each amino acid site of your
sequence, residue number, three- and one-letter residue code,
prediction, reliability estimate, and the number of residues from
related sequences projected onto this residue through the local
alignment procedure are shown in subsequent columns. Additionally, if
the STRIDE or DSSP assignments have been read using the options -x or
-y (and -z), the last column of the PREDATOR output will contain the
actual secondary structural assignment for your sequence if it
corresponds exactly to the one in the STRIDE or DSSP file (for
comparison). If the known assignment is not available, i.e., if you
did not use the -x or -y options, question signs will be output.</text>
<text lang="en">
Both output forms:
</text>
<text lang="en">
If option -h has been used, PREDATOR will show progress by printing
dots on the standard output. If your sequence has related sequences
with known 3D structure, PDB identifiers of these sequences will be
printed.
</text>
</comment>
<filenames>
<code proglang="python">'predator.out'</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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