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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
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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
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123 There are a number of protein families as well as functional or
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124 structural domains that cannot be detected using patterns due to their extreme
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125 sequence divergence, so the use of techniques based on weight matrices
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126 (also known as profiles) allows the detection of such proteins or domains.
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127 A profile is a table of position-specific amino acid weights and gap costs.
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128 The profile structure used in PROSITE is similar to but slightly more general
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129 (Bucher P. et al., 1996) than the one introduced by M. Gribskov and
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130 co-workers.
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131 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
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132
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133 **PRINTS**::
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134
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135 The PRINTS database houses a collection of protein family fingerprints.
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136 These are groups of motifs that together are diagnostically more
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137 powerful than single motifs by making use of the biological context inherent in a
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138 multiple-motif method. The fingerprinting method arose from the need for
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139 a reliable technique for detecting members of large, highly divergent
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140 protein super-families.
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141 FingerPRINTScan (Scordis P. et al., 1999).
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142
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143 **PFAM**::
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144
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145 Pfam is a database of protein domain families. Pfam contains curated
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146 multiple sequence alignments for each family and corresponding hidden
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147 Markov models (HMMs) (Eddy S.R., 1998).
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148 Profile hidden Markov models are statistical models of the primary
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149 structure consensus of a sequence family. The construction and use
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150 of Pfam is tightly tied to the HMMER software package.
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151 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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152 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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153
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154 **PRODOM**::
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155
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156 ProDom is a database of protein domain families obtained by automated
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157 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
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158 for analysing the domain arrangements of complex protein families and the
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159 homology relationships in modular proteins. ProDom families are built by
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160 an automated process based on a recursive use of PSI-BLAST homology
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161 searches.
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162 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
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163 and Yoann Beausse beausse@toulouse.inra.fr)
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164 a wrapper on top of the Blast package (Altschul S.F. et al., 1997).
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165
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166 **SMART**::
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167
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168 SMART (a Simple Modular Architecture Research Tool) allows the
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169 identification and annotation of genetically mobile domains and the
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170 analysis of domain architectures. These domains are extensively
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171 annotated with respect to phyletic distributions, functional class, tertiary
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172 structures and functionally important residues. SMART alignments are
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173 optimised manually and following construction of corresponding hidden Markov models (HMMs).
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174 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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175 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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176
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177 **TIGRFAMs**::
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178
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179 TIGRFAMs are a collection of protein families featuring curated multiple
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180 sequence alignments, Hidden Markov Models (HMMs) and associated
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181 information designed to support the automated functional identification
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182 of proteins by sequence homology. Classification by equivalog family
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183 (see below), where achievable, complements classification by orthologs,
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184 superfamily, domain or motif. It provides the information best suited
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185 for automatic assignment of specific functions to proteins from large
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186 scale genome sequencing projects.
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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 **PIR SuperFamily**::
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191
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192 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
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193 relationship of whole proteins.
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194 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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195 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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196
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197 **SUPERFAMILY**::
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198
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199 SUPERFAMILY is a library of profile hidden Markov models that represent
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200 all proteins of known structure, based on SCOP.
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201 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
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202 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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203 Optionally, predictions for coiled-coil, signal peptide cleavage sites
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204 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
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205 for details).
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206
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207 **GENE3D**::
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208
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209 Gene3D is supplementary to the CATH database. This protein sequence database
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210 contains proteins from complete genomes which have been clustered into protein
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211 families and annotated with CATH domains, Pfam domains and functional
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212 information from KEGG, GO, COG, Affymetrix and STRINGS.
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213 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
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214 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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215
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216 **PANTHER**::
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217
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218 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
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219 Classification System was designed to classify proteins (and their genes)
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220 in order to facilitate high-throughput analysis.
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221 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
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222 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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223 and blastall from the Blast package (Altschul S.F. et al., 1997).
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224
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225 ----------
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226 References
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227 ----------
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228
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229 Zdobnov EM, Apweiler R (2001)
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230 InterProScan an integration platform for the signature-recognition methods in InterPro.
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231 Bioinformatics 17, 847-848.
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232 http://dx.doi.org/10.1093/bioinformatics/17.9.847
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233
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234 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
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235 InterProScan: protein domains identifier.
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236 Nucleic Acids Research 33 (Web Server issue), W116-W120.
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237 http://dx.doi.org/10.1093/nar/gki442
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238
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239 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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240 InterPro: the integrative protein signature database.
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241 Nucleic Acids Research 37 (Database Issue), D224-228.
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242 http://dx.doi.org/10.1093/nar/gkn785
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243
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244
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245 **Galaxy Wrapper Author**::
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246
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247 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
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248 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
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249
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250 </help>
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251 </tool>
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