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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 tabular file in galaxy with 14 columns and can be easily concatenated or filtered.
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87
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88 ====== ================================================================ ======================================================================
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89 column example description
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90 ====== ================================================================ ======================================================================
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91 c1 NF00181542 the id of the input sequence
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92 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique)
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93 c3 272 the length of the sequence (in AA)
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94 c4 HMMPIR the anaysis method launched.
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95 c5 PIRSF001424 the database members entry for this match
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96 c6 Prephenate dehydratase the database member description for the entry
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97 c7 1 the start of the domain match
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98 c8 270 the end of the domain match
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99 c9 6.5e-141 the evalue of the match (reported by member database method)
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100 c10 T the status of the match (T: true, ?: unknown)
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101 c11 06-Aug-2005 the date of the run.
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102 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user)
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103 c13 Prephenate dehydratase with ACT region the description of the InterPro entry
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104 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry
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105 ====== ================================================================ ======================================================================
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106
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107 **Database updates**
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108
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109 Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases.
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110
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111 -----
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112 Tools
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113 -----
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114
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115 **PROSITE patterns**
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116 Some biologically significant amino acid patterns can be summarised in
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117 the form of regular expressions.
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118 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk).
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119
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120 **PROSITE profiles**
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121 There are a number of protein families as well as functional or
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122 structural domains that cannot be detected using patterns due to their extreme
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123 sequence divergence, so the use of techniques based on weight matrices
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124 (also known as profiles) allows the detection of such proteins or domains.
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125 A profile is a table of position-specific amino acid weights and gap costs.
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126 The profile structure used in PROSITE is similar to but slightly more general
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127 (Bucher P. et al., 1996) than the one introduced by M. Gribskov and
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128 co-workers.
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129 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
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130
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131 **PRINTS**
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132 The PRINTS database houses a collection of protein family fingerprints.
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133 These are groups of motifs that together are diagnostically more
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134 powerful than single motifs by making use of the biological context inherent in a
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135 multiple-motif method. The fingerprinting method arose from the need for
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136 a reliable technique for detecting members of large, highly divergent
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137 protein super-families.
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138 FingerPRINTScan (Scordis P. et al., 1999).
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139
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140 **PFAM**
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141 Pfam is a database of protein domain families. Pfam contains curated
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142 multiple sequence alignments for each family and corresponding hidden
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143 Markov models (HMMs) (Eddy S.R., 1998).
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144 Profile hidden Markov models are statistical models of the primary
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145 structure consensus of a sequence family. The construction and use
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146 of Pfam is tightly tied to the HMMER software package.
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147 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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148 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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149
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150 **PRODOM**
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151 ProDom is a database of protein domain families obtained by automated
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152 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
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153 for analysing the domain arrangements of complex protein families and the
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154 homology relationships in modular proteins. ProDom families are built by
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155 an automated process based on a recursive use of PSI-BLAST homology
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156 searches.
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157 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
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158 and Yoann Beausse beausse@toulouse.inra.fr)
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159 a wrapper on top of the Blast package (Altschul S.F. et al., 1997).
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160
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161 **SMART**
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162 SMART (a Simple Modular Architecture Research Tool) allows the
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163 identification and annotation of genetically mobile domains and the
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164 analysis of domain architectures. These domains are extensively
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165 annotated with respect to phyletic distributions, functional class, tertiary
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166 structures and functionally important residues. SMART alignments are
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167 optimised manually and following construction of corresponding hidden Markov models (HMMs).
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168 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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169 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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170
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171 **TIGRFAMs**
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172 TIGRFAMs are a collection of protein families featuring curated multiple
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173 sequence alignments, Hidden Markov Models (HMMs) and associated
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174 information designed to support the automated functional identification
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175 of proteins by sequence homology. Classification by equivalog family
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176 (see below), where achievable, complements classification by orthologs,
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177 superfamily, domain or motif. It provides the information best suited
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178 for automatic assignment of specific functions to proteins from large
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179 scale genome sequencing projects.
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180 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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181 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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182
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183 **PIR SuperFamily**
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184 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
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185 relationship of whole proteins.
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186 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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187 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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188
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189 **SUPERFAMILY**
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190 SUPERFAMILY is a library of profile hidden Markov models that represent
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191 all proteins of known structure, based on SCOP.
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192 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
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193 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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194 Optionally, predictions for coiled-coil, signal peptide cleavage sites
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195 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file for details).
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196
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197 **GENE3D**
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198 Gene3D is supplementary to the CATH database. This protein sequence database
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199 contains proteins from complete genomes which have been clustered into protein
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200 families and annotated with CATH domains, Pfam domains and functional
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201 information from KEGG, GO, COG, Affymetrix and STRINGS.
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202 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
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203 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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204
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205 **PANTHER**
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206 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
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207 Classification System was designed to classify proteins (and their genes)
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208 in order to facilitate high-throughput analysis.
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209 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
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210 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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211 and blastall from the Blast package (Altschul S.F. et al., 1997).
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212
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213 ----------
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214 References
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215 ----------
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216
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217 Zdobnov EM, Apweiler R (2001)
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218 InterProScan an integration platform for the signature-recognition methods in InterPro.
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219 Bioinformatics 17, 847-848.
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220 http://dx.doi.org/10.1093/bioinformatics/17.9.847
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221
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222 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
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223 InterProScan: protein domains identifier.
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224 Nucleic Acids Research 33 (Web Server issue), W116-W120.
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225 http://dx.doi.org/10.1093/nar/gki442
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226
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227 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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228 InterPro: the integrative protein signature database.
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229 Nucleic Acids Research 37 (Database Issue), D224-228.
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230 http://dx.doi.org/10.1093/nar/gkn785
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231
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232
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233 **Galaxy Wrapper Author**::
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234
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235 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
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236 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
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237
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238 </help>
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239 </tool>
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