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<?xml version="1.0" encoding="ISO-8859-1"?>
<!-- XML Authors: Corinne Maufrais and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>restrict</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>restrict</title>
<description>
<text lang="en">Report restriction enzyme cleavage sites in a nucleotide sequence</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/restrict.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:nucleic:restriction</category>
<command>restrict</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>EMBL</dataFormat>
<dataFormat>FASTA</dataFormat>
<dataFormat>GCG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>NBRF</dataFormat>
<dataFormat>PIR</dataFormat>
<dataFormat>RAW</dataFormat>
<dataFormat>SWISSPROT</dataFormat>
<dataFormat>GFF</dataFormat>
<card>1,n</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>e_datafile</name>
<prompt lang="en">Restriction enzyme data file (optional)</prompt>
<type>
<datatype>
<class>RestrictionEnzymeData</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="python">("", " -datafile=" + str(value))[value is not None]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>e_mfile</name>
<prompt lang="en">Restriction enzyme methylation data file (optional)</prompt>
<type>
<datatype>
<class>RestrictionEnzymeMethylationData</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="python">("", " -mfile=" + str(value))[value is not None ]</code>
</format>
<argpos>3</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sitelen</name>
<prompt lang="en">Minimum recognition site length (value from 2 to 20)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="python">("", " -sitelen=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 2 is required</text>
</message>
<code proglang="python">value >= 2</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 20 is required</text>
</message>
<code proglang="python">value <= 20</code>
</ctrl>
<argpos>4</argpos>
<comment>
<text lang="en">This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored.</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_enzymes</name>
<prompt lang="en">Comma separated enzyme list</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>all</value>
</vdef>
<format>
<code proglang="python">("", " -enzymes=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">The name 'all' reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as: 'HincII,hinfI,ppiI,hindiii'.
The case of the names is not important. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a '@' character in front of it, for example, '@enz.list'.
Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for.
An example of a file of enzyme names is:
! my enzymes
HincII, ppiII
! other enzymes
hindiii
HinfI
PpiI</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<parameter>
<name>e_min</name>
<prompt lang="en">Minimum cuts per re (value from 1 to 1000)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -min=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 1000 is required</text>
</message>
<code proglang="python">value <= 1000</code>
</ctrl>
<argpos>6</argpos>
<comment>
<text lang="en">This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_max</name>
<prompt lang="en">Maximum cuts per re</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2000000000</value>
</vdef>
<format>
<code proglang="python">("", " -max=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_solofragment</name>
<prompt lang="en">List individual enzymes with their fragments</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -solofragment")[ bool(value) ]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">This gives the fragment lengths of the forward sense strand produced by complete restriction by each restriction enzyme on its own. Results are added to the tail section of the report.</text>
</comment>
</parameter>
<parameter>
<name>e_single</name>
<prompt lang="en">Force single site only cuts</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -single")[ bool(value) ]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_blunt</name>
<prompt lang="en">Allow blunt end cutters</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noblunt", "")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">This allows those enzymes which cut at the same position on the forward and reverse strands to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_sticky</name>
<prompt lang="en">Allow sticky end cutters</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nosticky", "")[ bool(value) ]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_ambiguity</name>
<prompt lang="en">Allow ambiguous matches</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noambiguity", "")[ bool(value) ]</code>
</format>
<argpos>12</argpos>
<comment>
<text lang="en">This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered</text>
</comment>
</parameter>
<parameter>
<name>e_plasmid</name>
<prompt lang="en">Allow circular dna</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -plasmid")[ bool(value) ]</code>
</format>
<argpos>13</argpos>
<comment>
<text lang="en">If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_methylation</name>
<prompt lang="en">Use methylation data</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -methylation")[ bool(value) ]</code>
</format>
<argpos>14</argpos>
<comment>
<text lang="en">If this is set then RE recognition sites will not match methylated bases.</text>
</comment>
</parameter>
<parameter>
<name>e_commercial</name>
<prompt lang="en">Only enzymes with suppliers</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nocommercial", "")[ bool(value) ]</code>
</format>
<argpos>15</argpos>
<comment>
<text lang="en">If this is set, then only those enzymes with a commercial supplier will be searched for. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through 'all' the enzymes in the REBASE database. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_limit</name>
<prompt lang="en">Limits reports to one isoschizomer</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nolimit", "")[ bool(value) ]</code>
</format>
<argpos>16</argpos>
<comment>
<text lang="en">This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file 'embossre.equ', which is created by the program 'rebaseextract'. If you prefer different prototypes to be used, make a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching 'all' of them.</text>
</comment>
</parameter>
<parameter>
<name>e_alphabetic</name>
<prompt lang="en">Sort output alphabetically</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -alphabetic")[ bool(value) ]</code>
</format>
<argpos>17</argpos>
</parameter>
<parameter>
<name>e_fragments</name>
<prompt lang="en">Show fragment lengths</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -fragments")[ bool(value) ]</code>
</format>
<argpos>18</argpos>
<comment>
<text lang="en">This gives the fragment lengths of the forward sense strand produced by complete restriction using all of the input enzymes together. Results are added to the tail section of the report.</text>
</comment>
</parameter>
<parameter>
<name>e_name</name>
<prompt lang="en">Show sequence name</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -name")[ bool(value) ]</code>
</format>
<argpos>19</argpos>
</parameter>
<parameter>
<name>e_outfile</name>
<prompt lang="en">Name of the report file</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>restrict.report</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter>
<name>e_rformat_outfile</name>
<prompt lang="en">Choose the report output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>TABLE</value>
</vdef>
<vlist>
<velem>
<value>DASGFF</value>
<label>Dasgff</label>
</velem>
<velem>
<value>DBMOTIF</value>
<label>Dbmotif</label>
</velem>
<velem>
<value>DIFFSEQ</value>
<label>Diffseq</label>
</velem>
<velem>
<value>EMBL</value>
<label>Embl</label>
</velem>
<velem>
<value>EXCEL</value>
<label>Excel</label>
</velem>
<velem>
<value>FEATTABLE</value>
<label>Feattable</label>
</velem>
<velem>
<value>GENBANK</value>
<label>Genbank</label>
</velem>
<velem>
<value>GFF</value>
<label>Gff</label>
</velem>
<velem>
<value>LISTFILE</value>
<label>Listfile</label>
</velem>
<velem>
<value>MOTIF</value>
<label>Motif</label>
</velem>
<velem>
<value>NAMETABLE</value>
<label>Nametable</label>
</velem>
<velem>
<value>PIR</value>
<label>Pir</label>
</velem>
<velem>
<value>REGIONS</value>
<label>Regions</label>
</velem>
<velem>
<value>SEQTABLE</value>
<label>Seqtable</label>
</velem>
<velem>
<value>SIMPLE</value>
<label>Simple</label>
</velem>
<velem>
<value>SRS</value>
<label>Srs</label>
</velem>
<velem>
<value>SWISS</value>
<label>Swiss</label>
</velem>
<velem>
<value>TABLE</value>
<label>Table</label>
</velem>
<velem>
<value>TAGSEQ</value>
<label>Tagseq</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -rformat=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>21</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
<dataFormat>
<ref param="e_rformat_outfile">
</ref>
</dataFormat>
</type>
<precond>
<code proglang="python">e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'PIR', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']</code>
</precond>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>auto</name>
<prompt lang="en">Turn off any prompting</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">" -auto -stdout"</code>
</format>
<argpos>22</argpos>
</parameter>
</parameters>
</program>
|
