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1 <!--
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2 # =====================================================
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3 # $Id: ExtractPeptideSequenceContext.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $
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4 # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ExtractPeptideSequenceContext.xml $
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5 # $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $
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6 # $LastChangedRevision: 90 $
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7 # $LastChangedBy: pieter.neerincx@gmail.com $
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8 # =====================================================
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9 -->
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10 <tool id="ExtractPeptideSequenceContext1" version="0.1" name="Extract Peptide Context">
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11 <description>by mapping peptides back to proteins and extending them on both termini to include their sequence context.</description>
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12 <command interpreter="perl">ExtractPeptideSequenceContext.pl --db $db --dbf FASTA --f $fragments --icol $icol --pcol $pcol $strip --pepo $pepo --n $n --c $c --pc '$pc' --ll WARN</command>
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13 <inputs>
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14 <param name="fragments" type="data" format="tabular" label="Peptide sequences and their protein's identifiers"
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15 help="(in tab delimited format)"/>
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16 <param name="icol" type="data_column" value="1" data_ref="fragments" label="Protein identifier column"/>
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17 <param name="pcol" type="data_column" value="2" data_ref="fragments" label="Peptide sequence column"/>
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18 <!--
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19 <param name="icol" type="integer" value="1" label="Protein identifier column"/>
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20 <param name="pcol" type="integer" value="2" label="Peptide sequence column"/>
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21 -->
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22 <param name="strip" type="select">
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23 <label>Lowercase characters in the peptide sequences represent</label>
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24 <option value="--s">Modifications</option>
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25 <option value="">Amino acids</option>
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26 </param>
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27 <param name="db" type="data" format="fasta" label="Protein sequences"
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28 help="(in FASTA format)"/>
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29 <param name="n" type="integer" value="5" label="N-terminal sequence context length"/>
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30 <param name="c" type="integer" value="5" label="C-terminal sequence context length"/>
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31 <param name="pc" type="select" help="to fill positions in the sequence context when the protein was too short for a full length context.">
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32 <label>Padding character</label>
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33 <option value="-">dash</option>
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34 <option value=" ">space</option>
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35 <option value="">none</option>
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36 </param>
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37 </inputs>
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38 <outputs>
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39 <data name="pepo" format="tabular" label="Peptide sequence contexts for ${fragments.name}"/>
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40 </outputs>
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41 <!--
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42 <tests>
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43 <test>
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44 <param name="input" value="*.fasta"/>
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45 <param name="identifiers" value="*.txt"/>
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46 <output name="output" file="*.fasta"/>
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47 </test>
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48 </tests>
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49 -->
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50 <help>
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51
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52 .. role:: raw-html(raw)
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53 :format: html
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54
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55 .. class:: infomark
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56
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57 **What it does**
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58
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59 Map peptide sequences back to proteins and extend the peptides on both termini to include their sequence context.
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60
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61 :raw-html:`<object data="static/images/nbic_gmr/ExtractPeptideSequenceContext.svg" type="image/svg+xml" width="100%"/>`
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62
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63 ===================================================
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64 *Peptide sequences and their protein's identifiers*
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65 ===================================================
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66
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67 This file must contain at least peptides and accession numbers or IDs of the proteins the peptides were derived from. \
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68 The data must be in TAB delimited format and may contain other columns, which will be preserved in the output. \
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69 If a sequence context was found, it will be appended in a new column to the right of the existing columns. \
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70 When another sequence context was found for the same peptide, it will appended as an extra row in the output.
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71 Protein accession numbers / IDs must be in the same format as was used in the FASTA file with protein sequences (database). \
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72 The only exception to this rule is that accession numbers / IDs may be optionally suffixed with the peptide\'s position in its protein between brackets. \
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73 For example: CLH1_HUMAN[1612-1620] will be matched to CLH1_HUMAN in a FASTA file with protein sequences. \
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74 Amino acids in the petide sequences must be in uppercase.
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75
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76 ===============================================
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77 *Protein sequences*
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78 ===============================================
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79
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80 Input file containing all protein sequences in FASTA format. \
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81 This tool will look for any type of protein ID in the first part of FASTA sequence headers up until the first white space. \
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82 Optionally multiple IDs may be present separated with pipe symbols (|) or semicolons (;). \
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83 Optionally IDs may be prefixed with a database namespace and a colon (:). \
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84 For example the accession number P32234 as well as the ID 128UP_DROME would be recognized in both this sequence header:
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85
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86 >UniProtAcc:P32234|UniProtID:128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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87
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88 and in this one:
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89
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90 >P32234|128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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91
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92 ===================================================
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93 *N-terminal and C-terminal sequence context length*
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94 ===================================================
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95
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96 Integers specifying the length of the N-terminal and C-terminal sequence context to retrieve starting from the peptide termini. \
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97 So the total sequence context length for a peptide will be:
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98 (N-terminal sequence context) + (length of the peptide) + (C-terminal sequence context).
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99
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100 ===============================================
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101 *Padding character*
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102 ===============================================
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103
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104 Optional padding character to fill N-terminal or C-terminal positions in the sequence context, \
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105 when the protein was too short to get a complete sequence context. \
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106 Defaults to - a.k.a. dash or alignment gap character. \
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107
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108 -----
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109
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110 **Getting input data**
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111
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112 .. _my folder utility: http://mascotinternal.chem.uu.nl/mascot/cgi/uu_myfolder.pl
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113
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114 This tool requires \
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115 peptide sequences in TAB delimited format and \
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116 protein sequences from which the peptides were derived in FASTA format. \
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117 If your peptide sequences are not in TAB delimited format, you can convert from:
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118
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119 - FASTA format using *FASTA manipulation* -> *FASTA-to-Tabular*
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120 - A format using a different delimiter using *Text Manipulation* -> *Convert*
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121
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122 When your peptides were derived from a mass spectrometry experiment and identified with a search engine like Mascot, Sequest, etc.,\
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123 please make sure you provide the same FASTA database for this tool as the one used for your search.
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124 If you used Mascot hosted by the Biomolecular Mass Spectrometry and Proteomics Group @ Utrecht University, \
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125 you can use the `my folder utility`_ to download the FASTA databases from the Mascot server.
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126
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127 -----
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128
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129 **Examples**
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130
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131 Example input for peptides identified with a Mascot search, \
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132 some with phosphorylated residues indicated by pS, pT or pY \
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133 and in TAB delimited format::
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134
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135 sequence score peptide mr mass delta (abs) mass delta (ppm) all protein matches
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136 AGNAARDN 54.24 787.357254 -4.223E-5 -0.05334300253990 H2A1B_HUMAN[67-74]
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137 KLpSAAVVLI 11.48 912.600784 0.001608 1.7619971713721432 OSGI2_HUMAN[405-413]
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138 RAGIKVpTVA 23.01 913.570892 6.283E-5 0.06786555979719196 PARK7_HUMAN[28-36]
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139 KGGVVGIKVD 44.61 970.581146 -0.001214 -1.2507970147608864 P04075[101-110]
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140 KIKELQAF 11.87 975.575287 0.003907 4.00481649347068 O60882[71-78]
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141 KIpSGpTVNIR 57.17 986.587265 -0.002761 -2.798536022051734 SYTC_HUMAN[681-689]
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142 KLpYEALKF 17.54 1010.580032 0.004782 4.731935966057164 F105A_HUMAN[238-245]
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143 KLDApSEpSLR 31.31 1017.545441 -0.002377 -2.3360136110127785 CLH1_HUMAN[1612-1620]
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144
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145 ===============================================
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146 *Appending peptide sequence contexts*
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147 ===============================================
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148
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149 With these options:
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150
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151 - c6 as *Protein identifier column*
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152 - c1 as *Peptide sequence column*
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153 - 5 as *N-terminal sequence context length*
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154 - 5 as *C-terminal sequence context length*
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155 - a suitable FASTA database with *Protein sequences*
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156 - and everything else set to defaults
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157
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158 the example above will generate a result like this::
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159
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160 AGNAARDN 54.24 787.357254 -4.223E-5 -0.05334300253990 H2A1B_HUMAN[67-74] EILELAGNAARDNKKTRI
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161 KLpSAAVVLI 11.48 912.600784 0.001608 1.7619971713721432 OSGI2_HUMAN[405-413] LKKIFKLSAAVVLIGSHPN
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162 RAGIKVpTVA 23.01 913.570892 6.283E-5 0.06786555979719196 PARK7_HUMAN[28-36] VDVMRRAGIKVTVAGLAGK
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163 KGGVVGIKVD 44.61 970.581146 -0.001214 -1.2507970147608864 P04075[101-110] QVIKSKGGVVGIKVDKGVVP
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164 KIKELQAF 11.87 975.575287 0.003907 4.00481649347068 O60882[71-78] NSMIRKIKELQAFFGLQV
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165 KIpSGpTVNIR 57.17 986.587265 -0.002761 -2.798536022051734 SYTC_HUMAN[681-689] VGEKEKISGTVNIRTRDNK
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166 KLpYEALKF 17.54 1010.580032 0.004782 4.731935966057164 F105A_HUMAN[238-245] AILEYKLYEALKFIMLYQ
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167 KLDApSEpSLR 31.31 1017.545441 -0.002377 -2.3360136110127785 CLH1_HUMAN[1612-1620] LTKVDKLDASESLRKEEEQ
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168
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169 Note the header line was ignored.
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170
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171 </help>
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172 </tool>
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