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1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.2">
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2 <description>Interproscan functional predictions of ORFs</description>
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3 <command>
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4 ## The command is a Cheetah template which allows some Python based syntax.
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5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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6
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7 ## create temp directory
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8 #import tempfile, os
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9 #set $tfile = tempfile.mkstemp()[1]
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10
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11 sed 's/ /_/g' $input > $tfile;
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12
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13 ## Hack, because interproscan does not seem to produce gff output even if it is configured
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14 #if str($oformat) == "gff":
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15 #set $tfile2 = tempfile.mkstemp()[1]
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16 iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl 2>&1;
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17 converter.pl -format gff3 -input $tfile2 -output $output;
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18 rm $tfile2;
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19 #else
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20 iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl 2>&1;
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21 #end if
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22
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23 rm $tfile
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24
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="fasta" label="Protein Fasta File"/>
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28
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29 <param name="appl" type="select" format="text" label="Applications to run" help="Select your programm.">
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30 <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>
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31 <option value="seg">seg</option>
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32 <option value="signalp">signalp</option>
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33 <option value="tmhmm">tmhmm</option>
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34 <option value="fprintscan">fprintscan</option>
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35 <option value="patternscan">patternscan</option>
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36 <option value="profilescan">profilescan</option>
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37 <option value="superfamily">superfamily</option>
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38 <option value="hmmpir">hmmpir</option>
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39 <option value="hmmpfam">hmmpfam</option>
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40 <option value="hmmsmart">hmmsmart</option>
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41 <option value="hmmtigr">hmmtigr</option>
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42 <option value="hmmpanther">hmmpanther</option>
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43 <option value="hamap">hamap</option>
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44 <option value="gene3d">gene3d</option>
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45 <option value="coils">coils</option>
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46 <option value="blastprodom">blastprodom</option>
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47 </param>
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48
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49 <param name="oformat" type="select" label="Output format" help="Please select a output format.">
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50 <option value="gff">gff</option>
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51 <option value="raw" selected="true">raw</option>
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52 <option value="txt">txt</option>
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53 <option value="html">html</option>
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54 <option value="xml">xml</option>
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55 <option value="ebixml">EBI header on top of xml</option>
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56 </param>
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57
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58 </inputs>
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59 <outputs>
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60
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61 <data format="txt" name="output" label="Interproscan calculation on ${on_string}">
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62 <change_format>
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63 <when input="oformat" value="html" format="html"/>
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64 <when input="oformat" value="xml" format="xml"/>
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65 <when input="oformat" value="ebixml" format="xml"/>
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66 <when input="oformat" value="gff" format="gff"/>
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67 </change_format>
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68 </data>
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69
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70 </outputs>
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71 <requirements>
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72 </requirements>
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73 <help>
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74 **What it does**
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75
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76 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
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77 These include SCOP, CATH, PFAM and SUPERFAMILY.
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78
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79 **Input**
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80
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81 Required is a FASTA file containing ORF predictions. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores ``_`` by this tool before running with Interproscan.
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82
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83 **Output**
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84
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85 Example for the raw format.
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86 The output will consist of a file in Interproscan raw format, a tabular file in galaxy with 14 columns.
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87 This can be use to upload the data into a relational database or concatenation of different runs.
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88
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89 ====== ================================================================ ======================================================================
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90 column example description
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91 ====== ================================================================ ======================================================================
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92 c1 NF00181542 the id of the input sequence
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93 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique)
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94 c3 272 the length of the sequence (in AA)
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95 c4 HMMPIR the anaysis method launched.
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96 c5 PIRSF001424 the database members entry for this match
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97 c6 Prephenate dehydratase the database member description for the entry
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98 c7 1 the start of the domain match
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99 c8 270 the end of the domain match
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100 c9 6.5e-141 the evalue of the match (reported by member database method)
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101 c10 T the status of the match (T: true, ?: unknown)
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102 c11 06-Aug-2005 the date of the run.
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103 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user)
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104 c13 Prephenate dehydratase with ACT region the description of the InterPro entry
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105 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry
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106 ====== ================================================================ ======================================================================
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107
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108 **Database updates**
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109
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110 Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases.
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111
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112 -----
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113 Tools
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114 -----
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115
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116 **PROSITE patterns**
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117 Some biologically significant amino acid patterns can be summarised in
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118 the form of regular expressions.
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119 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk).
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120
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121 **PROSITE profiles**
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122 There are a number of protein families as well as functional or
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123 structural domains that cannot be detected using patterns due to their extreme
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124 sequence divergence, so the use of techniques based on weight matrices
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125 (also known as profiles) allows the detection of such proteins or domains.
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126 A profile is a table of position-specific amino acid weights and gap costs.
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127 The profile structure used in PROSITE is similar to but slightly more general
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128 (Bucher P. et al., 1996) than the one introduced by M. Gribskov and
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129 co-workers.
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130 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
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131
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132 **PRINTS**
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133 The PRINTS database houses a collection of protein family fingerprints.
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134 These are groups of motifs that together are diagnostically more
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135 powerful than single motifs by making use of the biological context inherent in a
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136 multiple-motif method. The fingerprinting method arose from the need for
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137 a reliable technique for detecting members of large, highly divergent
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138 protein super-families.
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139 FingerPRINTScan (Scordis P. et al., 1999).
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140
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141 **PFAM**
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142 Pfam is a database of protein domain families. Pfam contains curated
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143 multiple sequence alignments for each family and corresponding hidden
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144 Markov models (HMMs) (Eddy S.R., 1998).
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145 Profile hidden Markov models are statistical models of the primary
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146 structure consensus of a sequence family. The construction and use
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147 of Pfam is tightly tied to the HMMER software package.
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148 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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149 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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150
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151 **PRODOM**
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152 ProDom is a database of protein domain families obtained by automated
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153 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
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154 for analysing the domain arrangements of complex protein families and the
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155 homology relationships in modular proteins. ProDom families are built by
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156 an automated process based on a recursive use of PSI-BLAST homology
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157 searches.
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158 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
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159 and Yoann Beausse beausse@toulouse.inra.fr)
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160 a wrapper on top of the Blast package (Altschul S.F. et al., 1997).
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161
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162 **SMART**
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163 SMART (a Simple Modular Architecture Research Tool) allows the
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164 identification and annotation of genetically mobile domains and the
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165 analysis of domain architectures. These domains are extensively
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166 annotated with respect to phyletic distributions, functional class, tertiary
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167 structures and functionally important residues. SMART alignments are
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168 optimised manually and following construction of corresponding hidden Markov models (HMMs).
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169 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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170 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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171
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172 **TIGRFAMs**
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173 TIGRFAMs are a collection of protein families featuring curated multiple
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174 sequence alignments, Hidden Markov Models (HMMs) and associated
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175 information designed to support the automated functional identification
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176 of proteins by sequence homology. Classification by equivalog family
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177 (see below), where achievable, complements classification by orthologs,
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178 superfamily, domain or motif. It provides the information best suited
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179 for automatic assignment of specific functions to proteins from large
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180 scale genome sequencing projects.
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181 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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182 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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183
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184 **PIR SuperFamily**
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185 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
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186 relationship of whole proteins.
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187 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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188 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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189
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190 **SUPERFAMILY**
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191 SUPERFAMILY is a library of profile hidden Markov models that represent
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192 all proteins of known structure, based on SCOP.
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193 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
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194 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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195 Optionally, predictions for coiled-coil, signal peptide cleavage sites
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196 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file for details).
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197
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198 **GENE3D**
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199 Gene3D is supplementary to the CATH database. This protein sequence database
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200 contains proteins from complete genomes which have been clustered into protein
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201 families and annotated with CATH domains, Pfam domains and functional
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202 information from KEGG, GO, COG, Affymetrix and STRINGS.
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203 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
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204 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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205
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206 **PANTHER**
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207 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
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208 Classification System was designed to classify proteins (and their genes)
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209 in order to facilitate high-throughput analysis.
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210 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
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211 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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212 and blastall from the Blast package (Altschul S.F. et al., 1997).
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213
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214 ----------
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215 References
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216 ----------
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217
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218 Zdobnov EM, Apweiler R (2001)
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219 InterProScan an integration platform for the signature-recognition methods in InterPro.
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220 Bioinformatics 17, 847-848.
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221 http://dx.doi.org/10.1093/bioinformatics/17.9.847
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222
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223 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
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224 InterProScan: protein domains identifier.
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225 Nucleic Acids Research 33 (Web Server issue), W116-W120.
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226 http://dx.doi.org/10.1093/nar/gki442
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227
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228 Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)
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229 InterPro: the integrative protein signature database.
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230 Nucleic Acids Research 37 (Database Issue), D224-228.
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231 http://dx.doi.org/10.1093/nar/gkn785
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232
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233
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234 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
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235 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan
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236
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237
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238 **Galaxy Wrapper Author**::
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239
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240 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
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241 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
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242
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243 </help>
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244 </tool>
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