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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>pratt</name>
<version>2.1</version>
<doc>
<title>Pratt</title>
<description>
<text lang="en">Pattern discovery in sets of unaligned protein sequences</text>
</description>
<authors>K. Sturzrehm, I. Jonassen</authors>
<homepagelink>http://www.ii.uib.no/~inge/Pratt.html</homepagelink>
<sourcelink>ftp://ftp.ebi.ac.uk/pub/software/unix/pratt/</sourcelink>
</doc>
<category>sequence:protein:pattern</category>
<command>pratt</command>
</head>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">Sequence File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" fasta $value"</code>
<code proglang="python">" fasta "+str(value)</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Fasta format. One file containing all the sequences. One sequence is specified by</text>
<text lang="en">one line starting with '>' in position 1 and then the name of the sequence, and some lines containing the sequence in upper or lower case. The end of a sequence is identified by looking for either the start of a new sequence or the end of the file.</text>
</comment>
<example>
>seq1
HLKSEDEMKASEDLKKHKKKGHHEAEIKPLAQSHATKHKIPVKYLEFIS
SDLHAHKLRKRKLVKNMVL
>seq2
VEVFISEDDLKRKLVKNMVLDKDNKQHMLPKAGDTVTNYTLLGLVLVLI
WLIMQRKRKKKEDVSEENIQEIPKKELAASS
</example>
</parameter>
<paragraph>
<name>conservation</name>
<prompt lang="en">Pattern conservation parameters</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>CM</name>
<prompt lang="en">Minimum number of Sequences to Match (-CM)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -CM $value":""</code>
<code proglang="python">("" , " -CM " + str(value))[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be between 2 and 4</text>
</message>
<code proglang="perl">$value >= 2 and $value <= 4</code>
<code proglang="python">value >= 2 and value <= 4</code>
</ctrl>
<comment>
<text lang="en">Set the minimum number of sequences to match a pattern. Pratt will only report patterns that match at least the chosen number of the sequences that you have input. Pratt will not allow you to choose a value higher than the number of sequences input.</text>
</comment>
</parameter>
<parameter>
<name>Cpct</name>
<prompt lang="en">Minimum Percentage of Sequences to Match (-C%)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>100</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -C% $value":""</code>
<code proglang="python">("" , " -C% " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Set the minimum percentage of the input sequences that should match a pattern. If you set this to, say 80, Pratt will only report patterns matching at least 80 % of the sequences input.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>restrictions</name>
<prompt lang="en">Pattern restrictions parameters</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>PP</name>
<prompt lang="en">Position in sequence (-PP)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>off</value>
</vdef>
<vlist>
<velem>
<value>off</value>
<label>OFF</label>
</velem>
<velem>
<value>complete</value>
<label>Complete pattern match has to be in this area (complete)</label>
</velem>
<velem>
<value>start</value>
<label>Pattern match has to start in this area (start)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -PP $value":""</code>
<code proglang="python">("" , " -PP " + str(value))[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">You must give a file to define the area (PF)</text>
</message>
<code proglang="perl">$value eq $vdef or ($value ne $vdef and defined $PF)</code>
<code proglang="python">value == vdef or (value != vdef and PF is not None)</code>
</ctrl>
<comment>
<text lang="en"/>
</comment>
</parameter>
<parameter>
<name>PF</name>
<prompt lang="en">Restriction File name (if PP not off) (-PF)</prompt>
<type>
<datatype>
<class>RestrictionPattern</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$PP ne "off"</code>
<code proglang="python">PP != "off"</code>
</precond>
<format>
<code proglang="perl">" -PF $value"</code>
<code proglang="python">" -PF " + str(value)</code>
</format>
<comment>
<text lang="en">This file contains lines to restrict pattern searches to certain regions in a sequence, say ACE2_YEAST: </text>
<text lang="en">>ACE2_YEAST (100,200)</text>
</comment>
</parameter>
<parameter>
<name>PL</name>
<prompt lang="en">Maximum Pattern Length (-PL)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>50</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -PL $value":""</code>
<code proglang="python">("" , " -PL " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Allows you to set the maximum length of a pattern. The length of the pattern C-x(2,4)-[DE] is 1+4+1=6. </text>
</comment>
</parameter>
<parameter>
<name>PN</name>
<prompt lang="en">Maximum number of Pattern Symbols (-PN)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>50</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -PN $value":" "</code>
<code proglang="python">("" , " -PN " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Using this you can set the maximum number of symbols in a pattern. The pattern C-x(2,4)-[DE] has 2 symbols (C and [DE]).</text>
</comment>
</parameter>
<parameter>
<name>PX</name>
<prompt lang="en">Maximum number of consecutive x's (-PX)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -PX $value":""</code>
<code proglang="python">("" , " -PX " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Using this option you can set the maximum length of a wildcard.</text>
</comment>
<example>
x - 1
x(10) - 10
x(3,4) - 4
</example>
</parameter>
<parameter>
<name>FN</name>
<prompt lang="en">Maximum number of flexible spacers (-FN)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -FN $value":""</code>
<code proglang="python">("" , " -FN " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Using this option you can set the maximum number of flexible wildcards (matching a variable number of arbitrary sequence symbols). For instance x(2,4) is a flexible wildcard, and the pattern C-x(2,4)-[DE]-x(10)-F contains one flexible wildcard.</text>
</comment>
</parameter>
<parameter>
<name>FL</name>
<prompt lang="en">Maximum Flexibility (-FL)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -FL $value":""</code>
<code proglang="python">("" , " -FL " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">You can set the maximum flexibility of a flexible wildcard (matching a variable number of arbitrary sequence symbols). For instance x(2,4) and x(10,12) has flexibility 2, and x(10) has flexibility 0. Increasing FL will increase the time used by Pratt.</text>
</comment>
</parameter>
<parameter>
<name>FP</name>
<prompt lang="en">Maximum Flexibility Product (-FP)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -FP $value":""</code>
<code proglang="python">("" , " -FP " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en"> Using option FP you can set an upper limit on the product of a flexibilities for a pattern. This is related to the memory requirements of the search, and increasing the limit, increases the memory usage. Some patterns and the corresponding product of flexibilities.</text>
</comment>
<example>
C-x(2,4)-[DE]-x(10)-F - (4-2+1)*(10-10+1)= 3
C-x(2,4)-[DE]-x(10-14)-F - (4-2+1)*(14-10+1)= 3*5= 15
</example>
</parameter>
<parameter>
<name>BI</name>
<prompt lang="en">Input Pattern Symbol File? (-BI)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -BI on":""</code>
<code proglang="python">("" , " -BI on")[ value ]</code>
</format>
<comment>
<text lang="en">Using the B options (BN,BI,BF) on the menu you can control which pattern symbols will be used during the initial pattern search and during the refinement phase. The pattern symbols that can be used, are read from a file if the BI option is set, otherwise a default set will be used.</text>
<text lang="en">The default set has as the 20 first elements, the single amino acid symbols, and it also contains a set of ambiguous symbols, each containing amino acids that share some physio-chemical properties</text>
</comment>
</parameter>
<parameter>
<name>BF</name>
<prompt lang="en">Input Pattern Symbol File name (if BI on) (-BF)</prompt>
<type>
<datatype>
<class>PatternSymbol</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$BI</code>
<code proglang="python">BI</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -BF $value" : "-BF <xi:include href="../../Local/Services/Programs/Env/pratt_data.xml" xpointer="xpointer(/pratt_data/pattern/text())" />Pratt.sets.big" </code>
<code proglang="python">( " -BF <xi:include href="../../Local/Services/Programs/Env/pratt_data.xml" xpointer="xpointer(/pratt_data/pattern/text())" />Pratt.sets.big" , " -BF " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">In the file each symbol is given on a separate line concataining the letters that the symbol should match. For the example, only patterns with the symbols C and [DE] would be considered. During the initial search, pattern symbols corresponding to the first BN lines can be used.</text>
<text lang="en">default file is: Pratt.sets.big</text>
</comment>
<example>
C
DE
</example>
</parameter>
<parameter>
<name>BN</name>
<prompt lang="en">Number of Pattern Symbols Initial Search (-BN)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -BN $value":""</code>
<code proglang="python">("" , " -BN " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Increasing BN will slow down the search and increase the memory usage, but allow more ambiguous pattern symbols.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>scoring</name>
<prompt lang="en">Pattern Scoring parameters</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>S</name>
<prompt lang="en">Scoring (-S)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>info</value>
</vdef>
<vlist>
<velem>
<value>info</value>
<label>Information content (info)</label>
</velem>
<velem>
<value>mdl</value>
<label>Minimum Description Length (mdl)</label>
</velem>
<velem>
<value>tree</value>
<label>Diversity calculated from a dendrogram (tree)</label>
</velem>
<velem>
<value>dist</value>
<label>Distances matrix (dist)</label>
</velem>
<velem>
<value>ppv</value>
<label>Positive Predictive Value (ppv)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -S $value":""</code>
<code proglang="python">("" , " -S " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">The S option allows you to control the scoring of patterns. There are five possible scoring schemes to be used:</text>
<text lang="en">info: patterns are scored by their information content as defined in (Jonassen et al, 1995). Note that a pattern's score is independent of which sequences it matches.</text>
<text lang="en">mdl: patterns are scored by a Minimum Description Length principle derived scoring scheme, which is related to the one above, but penalises patterns scoring few sequences vs. patterns scoring many. Parameters Z0 to Z3 are required when this scoring scheme is used.</text>
<text lang="en">tree: a pattern is scored higher if it contains more information and/or if it matches more diverse sequences. The sequence diversity is calculated from a dendrogram which has to be input.</text>
<text lang="en">dist: similar to the tree scoring, except a matrix with pairwise the similarity between all pairs of input sequences are used instead of the tree. The matrix has to be input.</text>
<text lang="en">ppv: a measure of Positive Predictive Value - it is assumed that the input sequences constitute a family, and are all contained in the Swiss-Prot database. PPV measures how certain one can be that a sequence belongs to the family given that it matches the pattern.</text>
<text lang="en">For the last three scoring schemes (tree, dist, ppv), an input file is needed.</text>
</comment>
</parameter>
<parameter ismandatory="1">
<name>treefile</name>
<prompt lang="en">Tree File for Scoring equal to tree (-SF)</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
</type>
<precond>
<code proglang="perl">$S eq "tree"</code>
<code proglang="python">S == "tree"</code>
</precond>
<format>
<code proglang="perl">" -SF $value "</code>
<code proglang="python">" -SF " + str(value)</code>
</format>
</parameter>
<parameter ismandatory="1">
<name>distfile</name>
<prompt lang="en">Distances File if Scoring equal to dist (-SF)</prompt>
<type>
<datatype>
<class>PhylipDistanceMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$S eq "dist"</code>
<code proglang="python">S == "dist"</code>
</precond>
<format>
<code proglang="perl">" -SF $value; "</code>
<code proglang="python">" -SF " + str(value)</code>
</format>
<comment>
<text lang="en">A matrix with pairwise the similarity between all pairs of input sequences are used instead of the tree.</text>
</comment>
</parameter>
<parameter>
<name>uniprotdb</name>
<prompt lang="en">Swissprot file if Scoring equal to ppv (-SF)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>SWISSPROT</dataFormat>
</type>
<precond>
<code proglang="perl">$S eq "ppv"</code>
<code proglang="python">S == "ppv"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -SF $value" : " -SF <xi:include href="../../Local/Services/Programs/Env/pratt_data.xml" xpointer="xpointer(/pratt_data/db/text())" />" </code>
<code proglang="python">( " -SF <xi:include href="../../Local/Services/Programs/Env/pratt_data.xml" xpointer="xpointer(/pratt_data/db/text())" />" , " -SF " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Default: uniprot_sprot databank.</text>
</comment>
</parameter>
<paragraph>
<name>mdl_param</name>
<prompt lang="en">MDL parameters (Z0-Z3) (if MDL scoring)</prompt>
<precond>
<code proglang="perl">$S eq "mdl"</code>
<code proglang="python">S == "mdl"</code>
</precond>
<argpos>3</argpos>
<parameters>
<parameter ismandatory="1">
<name>Z0</name>
<prompt lang="en">Z0</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -Z0 $value" : "" </code>
<code proglang="python">( "" , " -Z0 " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter ismandatory="1">
<name>Z1</name>
<prompt lang="en">Z1</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -Z1 $value" : ""</code>
<code proglang="python">( "" , " -Z1 " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter ismandatory="1">
<name>Z2</name>
<prompt lang="en">Z2</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>3.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -Z2 $value" : ""</code>
<code proglang="python">( "" , " -Z2 " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter ismandatory="1">
<name>Z3</name>
<prompt lang="en">Z3</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10.00</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -Z3 $value" : ""</code>
<code proglang="python">( "" , " -Z3 " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>search</name>
<prompt lang="en">Search parameters</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>G</name>
<prompt lang="en">Pattern Graph from: (-G)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>seq</value>
</vdef>
<vlist>
<velem>
<value>seq</value>
<label>Sequence (seq)</label>
</velem>
<velem>
<value>al</value>
<label>Alignment (al)</label>
</velem>
<velem>
<value>query</value>
<label>Query</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -G $value":""</code>
<code proglang="python">("" , " -G " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">If G is set to al or query, another option GF is required allowing the user to give the name of a file containing a multiple sequence alignment (in Clustal W format), or a query sequence in FastA format (without annotation). Only patterns consistent with the alignment/matching the query sequence will be considered.</text>
</comment>
</parameter>
<parameter ismandatory="1">
<name>GF_ali</name>
<prompt lang="en">Alignment file (if G set to al) (-GF)</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>CLUSTAL</dataFormat>
</type>
<precond>
<code proglang="perl">$G eq "al"</code>
<code proglang="python">G == "al"</code>
</precond>
<format>
<code proglang="perl">" -GF $value"</code>
<code proglang="python">" -GF " + str(value)</code>
</format>
<comment>
<text lang="en">Alignment file must be in CLUSTALW format</text>
</comment>
</parameter>
<parameter ismandatory="1">
<name>GF_seq</name>
<prompt lang="en">Query sequence file (if G set query) (-GF)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">$G eq "query"</code>
<code proglang="python">G == "query"</code>
</precond>
<format>
<code proglang="perl">" -GF $value"</code>
<code proglang="python">" -GF " + str(value)</code>
</format>
<comment>
<text lang="en">Query file must be in Fasta format</text>
</comment>
</parameter>
<parameter>
<name>E</name>
<prompt lang="en">Search Greediness (-E)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>3</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -E $value":""</code>
<code proglang="python">("" , " -E " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Using the E parameter you can adjust the greediness of the search. Setting E to 0 (zero), the search will be exhaustive. Increasing E increases the greediness, and decreases the time used in the search.</text>
</comment>
</parameter>
<parameter>
<name>R</name>
<prompt lang="en">Pattern Refinement (-R)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -R off" : ""</code>
<code proglang="python">( " " , " -R off" )[ value ]</code>
</format>
<comment>
<text lang="en">When the R option is switched on, patterns found during the initial pattern search are input to a refinement algorithm where more ambiguous pattern symbols can be added. For instance the pattern C-x(4)-D might be refined to C-x-[ILV]-x-D-x(3)-[DEF]</text>
</comment>
</parameter>
<parameter>
<name>RG</name>
<prompt lang="en">Generalise ambiguous symbols (if Pattern Refinement on) (-RG)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$R</code>
<code proglang="python">R</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -RG on" : "" </code>
<code proglang="python">( "" , " -RG on" )[ value ]</code>
</format>
<comment>
<text lang="en">If the RG option is switched on, then ambiguous symbols listed in the symbols file (or in the default symbol set -- see help for option B), are used. If RG is off, only the letters needed to match the input sequences are included in the ambiguous pattern positions.</text>
<text lang="en">For example, if [ILV] is a listed allowed symbol, and [IL] is not, [IL] can be included in a pattern if RG is off, but if RG is on, the full symbol [ILV] will be included instead.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>OP</name>
<prompt lang="en">PROSITE Pattern Format (-OP)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -OP off " : ""</code>
<code proglang="python">( "" , " -OP off " )[ value ]</code>
</format>
<comment>
<text lang="en">When switched on, patterns will be output in PROSITE style (for instance C-x(2,4)-[DE]). When switched off, patterns are output in a simpler consensus pattern style (for instance Cxx--[DE] where x matches exactly one arbitrary sequence symbol and - matches zero or one arbitrary sequence symbol).</text>
</comment>
</parameter>
<parameter>
<name>ON</name>
<prompt lang="en">Maximum number patterns (-ON)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>50</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -ON $value":""</code>
<code proglang="python">("" , " -ON " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Set the maximum number of patterns to be found by Pratt</text>
</comment>
</parameter>
<parameter>
<name>OA</name>
<prompt lang="en">Maximum number Alignments (-OA)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>50</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -OA $value":""</code>
<code proglang="python">("" , " -OA " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Set the max. nr of patterns for which Pratt is to produce an alignment of the sequence segments matching it.</text>
</comment>
</parameter>
<parameter>
<name>M</name>
<prompt lang="en">Print Patterns in sequences (-M)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -M off " : ""</code>
<code proglang="python">( " " , " -M off" )[ value ]</code>
</format>
<comment>
<text lang="en">If the M option is set, then Pratt will print out the location of the sequence segments matching each of the (maximum 52) best patterns. The patterns are given labels A, B,...Z,a,b,...z in order of decreasing pattern score. Each sequence is printed on a line, one character per K-tuple in the sequence. If pattern with label C matches the third K-tuple in a sequence C is printed out. If several patterns match in the same K-tuple, only the best will be printed.</text>
</comment>
</parameter>
<parameter>
<name>MR</name>
<prompt lang="en">Ratio for printing (-MR)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$M</code>
<code proglang="python">M</code>
</precond>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -MR $value":""</code>
<code proglang="python">("" , " -MR " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Sets the K value (ratio) used for printing the summary information about where in each sequence the pattern matches are found.</text>
</comment>
</parameter>
<parameter>
<name>MV</name>
<prompt lang="en">Print vertically (-MV)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$M</code>
<code proglang="python">M</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -MV on " : "" </code>
<code proglang="python">( "" , " -MV on " )[ value ]</code>
</format>
<comment>
<text lang="en">If set, the output is printed vertically instead of horizontally, vertical output can be better for large sequence sets.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfiles</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.pat"</code>
<code proglang="python">"*.pat"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>report</name>
<prompt lang="en">Report output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"report"</code>
<code proglang="python">"report"</code>
</filenames>
</parameter>
</parameters>
</program>
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