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1 <?xml version="1.0" encoding="ISO-8859-1"?>
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2 <xsl:stylesheet version="1.0"
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3 xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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4 xmlns:cis="http://zlab.bu.edu/schema/cisml"
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5 xmlns:fimo="http://noble.gs.washington.edu/schema/cisml"
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6 xmlns:mem="http://noble.gs.washington.edu/meme"
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7 >
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8
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9 <xsl:output method="html" indent="yes"
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10 doctype-public="-//W3C//DTD HTML 4.01 Transitional//EN"
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11 doctype-system="http://www.w3.org/TR/html4/loose.dtd"
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12 />
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13
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14 <!-- Stylesheet processing starts here -->
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15 <xsl:template match="/fimo">
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16 <html>
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17 <xsl:call-template name="html_head"/>
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18 <body bgcolor='#D5F0FF'>
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19 <a name="top_buttons"></a>
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20 <hr />
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21 <table summary="buttons" align="left" cellspacing="0">
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22 <tr>
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23 <td bgcolor="#00FFFF">
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24 <a href='#database_and_motifs'><b>Database and Motifs</b></a>
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25 </td>
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26 <td bgcolor="#DDFFDD">
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27 <a href="#sec_i"><b>High-scoring Motif Occurences</b></a>
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28 </td>
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29 <td bgcolor="#DDDDFF">
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30 <a href="#debugging_information"><b>Debugging Information</b></a>
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31 </td>
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32 </tr>
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33 </table>
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34 <br />
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35 <br />
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36 <!-- Create the various sub-sections of the document -->
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37 <xsl:call-template name="version"/>
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38 <xsl:call-template name="database_and_motifs"/>
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39 <xsl:call-template name="high_scoring_motif_occurrences"/>
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40 <!-- Diagrams and annotations break for long sequences
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41 (H. sap. chr21 for example -->
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42 <!--
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43 <xsl:call-template name="motif_diagrams"/>
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44 <xsl:call-template name="annotations"/>
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45 -->
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46 <xsl:call-template name="debugging_information"/>
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47 <!-- Buttons are pointless since there is only one section
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48 <xsl:call-template name="button_help"/>
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49 -->
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50 </body>
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51 </html>
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52 </xsl:template>
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53
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54 <xsl:template name="html_head">
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55 <!-- This template prints the HTML head block, including the document level CSS. -->
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56 <head>
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57 <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
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58 <title>FIMO Results</title>
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59 <style type="text/css">
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60 td.left {text-align: left;}
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61 td.right {text-align: right; padding-right: 1cm;}
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62 </style>
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63 </head>
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64 </xsl:template>
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65
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66 <xsl:template name="version">
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67 <!--
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68 This template prints the HTML describing the version of FIMO
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69 that generated this document.
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70 -->
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71 <hr />
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72 <center>
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73 <big><b>FIMO - Motif search tool</b></big>
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74 </center>
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75 <hr />
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76 <p>
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77 FIMO version <xsl:value-of select="@version"/>,
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78 (Release date: <xsl:value-of select="@release"/>)
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79 </p>
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80 <p>
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81 For further information on how to interpret these results
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82 or to get a copy of the FIMO software please access
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83 <a href="http://meme.nbcr.net">http://meme.nbcr.net</a>
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84 </p>
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85 <p>If you use FIMO in your research, please cite the following paper:<br />
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86 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
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87 "FIMO: Scanning for occurrences of a given motif",
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88 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
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89 </p>
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90 </xsl:template>
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91
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92 <xsl:template name="reference">
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93 <!-- This template prints the instructions for citing FIMO. -->
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94 <hr/>
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95 <center>
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96 <a name="reference"/>
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97 <big><b>REFERENCE</b></big>
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98 </center>
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99 <hr/>
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100 <p>
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101 If you use this program in your research, please cite:
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102 </p>
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103 <p>
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104 </p>
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105 </xsl:template>
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106
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107 <xsl:template name="database_and_motifs">
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108 <!--
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109 This template prints the HTML descibing the input sequences
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110 and motifs that were used to generate this document.
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111 -->
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112 <hr/>
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113 <center>
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114 <big>
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115 <b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b>
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116 </big>
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117 </center>
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118 <hr/>
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119 <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
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120 <p>
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121 DATABASE
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122 <xsl:value-of select="/fimo/settings/setting[@name='sequence file name']"/>
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123 <br />
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124 Database contains
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125 <xsl:value-of select="/fimo/sequence-data/@num-sequences"/>
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126 sequences,
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127 <xsl:value-of select="/fimo/sequence-data/@num-residues"/>
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128 residues
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129 </p>
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130 <p>
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131 MOTIFS
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132 <xsl:value-of select="/fimo/settings/setting[@name='MEME file name']"/>
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133 <xsl:text> </xsl:text>
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134 (<xsl:value-of select="/fimo/alphabet"/>)
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135 <table>
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136 <thead>
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137 <tr>
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138 <th style="border-bottom: 1px dashed;">MOTIF</th>
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139 <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
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140 <th style="border-bottom: 1px dashed; padding-left: 1em;" align="left">
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141 BEST POSSIBLE MATCH
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142 </th>
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143 </tr>
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144 </thead>
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145 <tbody>
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146 <xsl:for-each select="/fimo/motif">
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147 <tr>
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148 <td align="right"><xsl:value-of select="./@name"/></td>
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149 <td align="right" style="padding-left: 1em;"><xsl:value-of select="./@width"/></td>
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150 <td align="left" style="padding-left: 1em;">
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151 <xsl:value-of select="./@best-possible-match"/>
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152 </td>
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153 </tr>
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154 </xsl:for-each>
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155 </tbody>
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156 </table>
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157 </p>
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158 <p>
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159 Random model letter frequencies
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160 (from <xsl:value-of select="/fimo/background/@source"/>):
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161 <br />
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162 <xsl:call-template name="bg_freq"/>
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163 </p>
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164 </div>
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165 </xsl:template>
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166
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167 <xsl:template name="bg_freq">
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168 <!-- This template prints the HTML listing the background frequencies for each symbol in the alphabet. -->
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169 <xsl:for-each select="/fimo/background/value">
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170 <xsl:value-of select="./@letter"/>
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171 <xsl:text> </xsl:text>
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172 <xsl:value-of select="format-number(., '0.000')"/>
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173 <xsl:text> </xsl:text>
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174 <!-- For amino acids insert a line break very 9 characters. -->
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175 <xsl:variable name="letter_index" select="position()" />
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176 <xsl:if test="$letter_index mod 9 = 0">
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177 <xsl:text> </xsl:text>
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178 <br/>
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179 <xsl:text> </xsl:text>
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180 </xsl:if>
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181 </xsl:for-each>
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182 </xsl:template>
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183
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184 <xsl:template name="high_scoring_motif_occurrences">
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185 <xsl:variable name="alphabet">
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186 <xsl:value-of select="/fimo/alphabet"/>
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187 </xsl:variable>
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188 <xsl:variable name="num_qvalues">
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189 <xsl:value-of
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190 select="count(document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/cis:matched-element/mem:qvalue)"/>
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191 </xsl:variable>
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192 <!-- This template prints the matches to the pattern. -->
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193 <hr/>
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194 <center>
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195 <big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big>
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196 </center>
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197 <hr/>
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198 <ul>
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199 <li> Each of the following
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200 <xsl:value-of select="count(document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/cis:matched-element)"/>
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201 motif occurrences has
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202 <xsl:choose>
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203 <xsl:when test="/fimo/settings/setting[@name='output q-threshold set'] = 'true'">
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204 q-value less than
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205 <xsl:value-of select="/fimo/settings/setting[@name='output q-value threshold' = 'true']"/>
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206 </xsl:when>
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207 <xsl:otherwise>
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208 p-value less than
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209 <xsl:value-of select="/fimo/settings/setting[@name='output p-value threshold']"/>
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210 </xsl:otherwise>
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211 </xsl:choose>
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212 </li>
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213 <li> The p-value of a motif occurrence is defined as the
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214 probability of a random sequence of the same length as the motif
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215 matching that position of the sequence with as good or better a score.
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216 </li>
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217 <li> The score for the match of a position in a sequence to a motif
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218 is computed by summing the appropriate entries from each column of
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219 the position-dependent scoring matrix that represents the motif.
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220 </li>
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221 <xsl:if test="$num_qvalues > 0">
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222 <li> The q-value of a motif occurrence is defined as the
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223 false discovery rate if the occurrence is accepted as significant.
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224 </li>
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225 </xsl:if>
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226 <li>The table is sorted by increasing p-value.</li>
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227 <li>If the start position is larger than the end position,
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228 the motif occurrence is on the reverse strand.
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229 </li>
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230 </ul>
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231 <table border="1">
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232 <thead>
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233 <tr>
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234 <th>Motif</th>
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235 <th>Sequence Name</th>
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236 <xsl:if test="$alphabet='nucleotide'">
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237 <th>Strand</th>
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238 </xsl:if>
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239 <th>Start</th>
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240 <th>End</th>
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241 <th>p-value</th>
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242 <xsl:if test="$num_qvalues > 0">
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243 <th>q-value</th>
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244 </xsl:if>
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245 <th>Matched Sequence</th>
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246 </tr>
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247 </thead>
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248 <tbody>
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249 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/cis:matched-element">
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250 <xsl:sort select="@pvalue" data-type="number" order="ascending"/>
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251 <xsl:variable name="seq_name" select="../@name"/>
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252 <tr>
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253 <td align="left">
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254 <a name="occurrences_{$seq_name}"><xsl:value-of select="../../@name"/></a>
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255 </td>
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256 <td align="left">
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257 <xsl:value-of select="../@name"/>
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258 </td>
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259 <!-- start and stop positions -->
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260 <!-- CISML uses start > stop to indicate - strand -->
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261 <!-- For HTML we want start < stop, indicate strand in strand column -->
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262 <xsl:if test="$alphabet='nucleotide'">
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263 <xsl:choose>
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264 <xsl:when test="@start > @stop">
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265 <!-- start > stop so - strand -->
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266 <td align="center"><xsl:text>−</xsl:text></td>
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267 </xsl:when>
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268 <xsl:otherwise>
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269 <td align="center"><xsl:text>+</xsl:text></td>
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270 </xsl:otherwise>
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271 </xsl:choose>
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272 </xsl:if>
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273 <xsl:choose>
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274 <xsl:when test="@start > @stop">
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275 <!-- start > stop so - strand -->
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276 <td align="left">
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277 <xsl:value-of select="@stop"/>
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278 </td>
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279 <td align="left">
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280 <xsl:value-of select="@start"/>
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281 </td>
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282 </xsl:when>
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283 <xsl:otherwise>
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284 <td align="left">
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285 <xsl:value-of select="@start"/>
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286 </td>
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287 <td align="left">
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288 <xsl:value-of select="@stop"/>
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289 </td>
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290 </xsl:otherwise>
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291 </xsl:choose>
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292 <td align="left">
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293 <xsl:value-of select="@pvalue"/>
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294 </td>
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295 <xsl:if test="$num_qvalues > 0">
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296 <td align="left">
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297 <xsl:value-of select="./mem:qvalue"/>
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298 </td>
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299 </xsl:if>
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300 <td align="left">
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301 <code style="font-size: x-large;"><xsl:value-of select="./cis:sequence"/></code>
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302 </td>
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303 </tr>
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304 </xsl:for-each>
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305 </tbody>
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306 </table>
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307 </xsl:template>
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308
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309 <xsl:template name="motif_diagrams">
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310 <!--
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311 This template draws the bead-on-string diagram for each
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312 of the scanned sequence.
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313 -->
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314 <hr/>
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315 <center>
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316 <big><b><a name="sec_ii">SECTION II: MOTIF DIAGRAMS</a></b></big>
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317 </center>
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318 <hr/>
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319 <table border="1">
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320 <thead>
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321 <tr>
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322 <th align="left"><br/>Name</th>
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323 <th align="left"><br/>Motifs</th>
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324 <th></th>
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325 </tr>
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326 </thead>
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327 <tbody>
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328 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[not (@name = preceding::cis:scanned-sequence/@name)]">
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329 <xsl:sort select="@name" order="ascending"/>
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330 <xsl:variable name="sequence_width" select="@length"/>
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331 <xsl:variable name="sequence_name" select="@name"/>
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332 <tr>
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333 <td><a name="diagram_{$sequence_name}"><xsl:value-of select="$sequence_name"/></a></td>
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334 <td>
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335 <table>
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336 <tr>
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337 <xsl:call-template name="draw_diagram_for_sequence">
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338 <xsl:with-param name="sequence_name" select="$sequence_name"/>
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339 <xsl:with-param name="sequence_width" select="@length"/>
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340 </xsl:call-template>
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341 </tr>
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342 </table>
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343 </td>
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344 </tr>
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345 </xsl:for-each>
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346 <tr>
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347 <td rowspan="2" style="color: blue;">SCALE</td>
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348 <td>
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349 <table>
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350 <tr>
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351 <td>
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352 <xsl:call-template name="ticks">
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353 <xsl:with-param name="count" select="1"/>
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354 <xsl:with-param name="limit">
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355 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/@length">
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356 <xsl:sort data-type="number" order="descending"/>
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357 <xsl:if test="position()=1"><xsl:value-of select="."/></xsl:if>
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358 </xsl:for-each>
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359 </xsl:with-param>
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360 </xsl:call-template>
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361 </td>
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362 </tr>
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363 <tr>
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364 <td>
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365 <xsl:call-template name="scale">
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366 <xsl:with-param name="count" select="1"/>
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367 <xsl:with-param name="limit">
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368 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/@length">
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369 <xsl:sort data-type="number" order="descending"/>
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370 <xsl:if test="position()=1"><xsl:value-of select="."/></xsl:if>
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371 </xsl:for-each>
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372 </xsl:with-param>
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373 </xsl:call-template>
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374 </td>
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375 </tr>
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376 </table>
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377 </td>
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378 </tr>
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379 </tbody>
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380 </table>
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381 </xsl:template>
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382
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383 <xsl:template name="draw_diagram_for_sequence">
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384 <!--
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385 This template draws the bead-on-string diagram for
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386 a single sequence.
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387 -->
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388 <xsl:param name="sequence_name"/>
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389 <xsl:param name="sequence_width"/>
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390 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name = $sequence_name]/cis:matched-element">
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391 <xsl:sort select="number(@start)" data-type="number" order="ascending"/>
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392 <xsl:variable name="starting">
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393 <xsl:choose>
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394 <xsl:when test="number(@start) < number(@stop)">
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395 <xsl:value-of select="@start"/>
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396 </xsl:when>
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397 <xsl:otherwise>
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398 <xsl:value-of select="@stop"/>
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399 </xsl:otherwise>
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400 </xsl:choose>
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401 </xsl:variable>
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402 <xsl:variable name="ending">
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403 <xsl:choose>
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404 <xsl:when test="number(@start) < number(@stop)">
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405 <xsl:value-of select="@stop"/>
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406 </xsl:when>
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407 <xsl:otherwise>
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408 <xsl:value-of select="@start"/>
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409 </xsl:otherwise>
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410 </xsl:choose>
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411 </xsl:variable>
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412 <xsl:variable name="current_element" select="position()"/>
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413 <xsl:variable name="previous_end">
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414 <xsl:choose>
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415 <xsl:when test="position() = 1">0</xsl:when>
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416 <xsl:otherwise>
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417 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name = $sequence_name]/cis:matched-element">
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418 <xsl:sort select="number(@start)" data-type="number" order="ascending"/>
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419 <xsl:if test="position() = ($current_element - 1)">
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420 <xsl:choose>
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421 <xsl:when test="number(@start) < number(@stop)">
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422 <xsl:value-of select="@stop"/>
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423 </xsl:when>
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424 <xsl:otherwise>
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425 <xsl:value-of select="@start"/>
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426 </xsl:otherwise>
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427 </xsl:choose>
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428 </xsl:if>
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429 </xsl:for-each>
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430 </xsl:otherwise>
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431 </xsl:choose>
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432 </xsl:variable>
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433 <xsl:variable name="motif_name">
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434 <xsl:value-of select="../../@name"/>
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435 </xsl:variable>
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436 <xsl:variable name="motif_index">
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437 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern">
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438 <xsl:if test="@name = $motif_name"><xsl:value-of select="position()"/></xsl:if>
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439 </xsl:for-each>
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440 <xsl:value-of select="@name"/>
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441 </xsl:variable>
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442 <xsl:variable name="motif_color">
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443 <xsl:call-template name="pick_color">
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444 <xsl:with-param name="index" select="$motif_index"/>
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445 </xsl:call-template>
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446 </xsl:variable>
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447 <xsl:variable name="font_color">
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448 <xsl:call-template name="pick_font_color">
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449 <xsl:with-param name="index" select="$motif_index"/>
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450 </xsl:call-template>
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451 </xsl:variable>
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452 <xsl:variable name="strand">
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453 <xsl:choose>
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454 <xsl:when test="number(@start) < number(@stop)">
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455 <xsl:text>+</xsl:text>
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456 </xsl:when>
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457 <xsl:otherwise>
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458 <xsl:text>-</xsl:text>
|
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459 </xsl:otherwise>
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460 </xsl:choose>
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461 </xsl:variable>
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|
462 <xsl:variable name="alphabet" select="document('fimo.xml')/fimo/alphabet"/>
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463 <td style="width: {2 * ($starting - $previous_end) }px;"><hr size="4" noshade="noshade"/></td>
|
|
|
464 <td style="width: {2 * ($ending - $starting)}px; background: {$motif_color}; color: {$font_color}; text-align: center;">
|
|
|
465 <xsl:if test="$alphabet = 'nucleotide'"><xsl:value-of select="$strand"/></xsl:if>
|
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|
466 <xsl:value-of select="../../@name"/>
|
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|
467 </td>
|
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|
468 <xsl:if test="position() = last()">
|
|
|
469 <td style="width: {2 * ($sequence_width - $ending) }px;"><hr size="4" noshade="noshade"/></td>
|
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|
470 </xsl:if>
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|
471 </xsl:for-each>
|
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|
472 </xsl:template>
|
|
|
473
|
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474 <xsl:template name="ticks">
|
|
|
475 <!--
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|
476 This template is used to print the tick marks in the
|
|
|
477 scale at the bottom of the bead-on-string daigrams.
|
|
|
478 -->
|
|
|
479 <xsl:param name="count" select="1"/>
|
|
|
480 <xsl:param name="limit" select="1"/>
|
|
|
481 <xsl:if test="$count < $limit">
|
|
|
482 <td style="width: 50px;" align="left"><font color="blue">|</font></td>
|
|
|
483 <xsl:call-template name="ticks">
|
|
|
484 <xsl:with-param name="count" select="$count + 24"/>
|
|
|
485 <xsl:with-param name="limit" select="$limit"/>
|
|
|
486 </xsl:call-template>
|
|
|
487 </xsl:if>
|
|
|
488 </xsl:template>
|
|
|
489
|
|
|
490 <xsl:template name="scale">
|
|
|
491 <!--
|
|
|
492 This template is used to print the text in the
|
|
|
493 scale at the bottom of the bead-on-string daigrams.
|
|
|
494 -->
|
|
|
495 <xsl:param name="count" select="1"/>
|
|
|
496 <xsl:param name="limit" select="1"/>
|
|
|
497 <xsl:if test="$count < $limit">
|
|
|
498 <td style="width: 50px;" align="left"><font color="blue"><xsl:value-of select="$count"/></font></td>
|
|
|
499 <xsl:if test="$count = 1">
|
|
|
500 <xsl:call-template name="scale">
|
|
|
501 <xsl:with-param name="limit" select="$limit"/>
|
|
|
502 <xsl:with-param name="count" select="$count + 24"/>
|
|
|
503 </xsl:call-template>
|
|
|
504 </xsl:if>
|
|
|
505 <xsl:if test="$count > 1">
|
|
|
506 <xsl:call-template name="scale">
|
|
|
507 <xsl:with-param name="limit" select="$limit"/>
|
|
|
508 <xsl:with-param name="count" select="$count + 25"/>
|
|
|
509 </xsl:call-template>
|
|
|
510 </xsl:if>
|
|
|
511 </xsl:if>
|
|
|
512 </xsl:template>
|
|
|
513
|
|
|
514 <xsl:template name="pick_color">
|
|
|
515 <!--
|
|
|
516 This template is used to set the color of motif markers
|
|
|
517 in the bead-on-string diagrams.
|
|
|
518 -->
|
|
|
519 <xsl:param name="index" select="1"/>
|
|
|
520 <xsl:choose>
|
|
|
521 <xsl:when test="($index mod 16) = 0">white</xsl:when>
|
|
|
522 <xsl:when test="($index mod 16) = 1">aqua</xsl:when>
|
|
|
523 <xsl:when test="($index mod 16) = 2">blue</xsl:when>
|
|
|
524 <xsl:when test="($index mod 16) = 3">red</xsl:when>
|
|
|
525 <xsl:when test="($index mod 16) = 4">fuchsia</xsl:when>
|
|
|
526 <xsl:when test="($index mod 16) = 5">yellow</xsl:when>
|
|
|
527 <xsl:when test="($index mod 16) = 6">lime</xsl:when>
|
|
|
528 <xsl:when test="($index mod 16) = 7">teal</xsl:when>
|
|
|
529 <xsl:when test="($index mod 16) = 8">#444444</xsl:when>
|
|
|
530 <xsl:when test="($index mod 16) = 9">green</xsl:when>
|
|
|
531 <xsl:when test="($index mod 16) = 10">silver</xsl:when>
|
|
|
532 <xsl:when test="($index mod 16) = 11">purple</xsl:when>
|
|
|
533 <xsl:when test="($index mod 16) = 12">olive</xsl:when>
|
|
|
534 <xsl:when test="($index mod 16) = 13">navy</xsl:when>
|
|
|
535 <xsl:when test="($index mod 16) = 14">maroon</xsl:when>
|
|
|
536 <xsl:when test="($index mod 16) = 15">black</xsl:when>
|
|
|
537 </xsl:choose>
|
|
|
538 </xsl:template>
|
|
|
539
|
|
|
540 <xsl:template name="pick_font_color">
|
|
|
541 <!--
|
|
|
542 This template is used to set the font color in motif markers
|
|
|
543 in the bead-on-string diagrams.
|
|
|
544 -->
|
|
|
545 <xsl:param name="index" select="1"/>
|
|
|
546 <xsl:choose>
|
|
|
547 <xsl:when test="($index mod 16) = 0">black</xsl:when>
|
|
|
548 <xsl:when test="($index mod 16) = 1">black</xsl:when>
|
|
|
549 <xsl:when test="($index mod 16) = 2">white</xsl:when>
|
|
|
550 <xsl:when test="($index mod 16) = 3">black</xsl:when>
|
|
|
551 <xsl:when test="($index mod 16) = 4">black</xsl:when>
|
|
|
552 <xsl:when test="($index mod 16) = 5">black</xsl:when>
|
|
|
553 <xsl:when test="($index mod 16) = 6">black</xsl:when>
|
|
|
554 <xsl:when test="($index mod 16) = 7">white</xsl:when>
|
|
|
555 <xsl:when test="($index mod 16) = 8">white</xsl:when>
|
|
|
556 <xsl:when test="($index mod 16) = 9">black</xsl:when>
|
|
|
557 <xsl:when test="($index mod 16) = 10">black</xsl:when>
|
|
|
558 <xsl:when test="($index mod 16) = 11">white</xsl:when>
|
|
|
559 <xsl:when test="($index mod 16) = 12">white</xsl:when>
|
|
|
560 <xsl:when test="($index mod 16) = 13">white</xsl:when>
|
|
|
561 <xsl:when test="($index mod 16) = 14">white</xsl:when>
|
|
|
562 <xsl:when test="($index mod 16) = 15">white</xsl:when>
|
|
|
563 </xsl:choose>
|
|
|
564 </xsl:template>
|
|
|
565
|
|
|
566 <xsl:template name="annotations">
|
|
|
567 <!--
|
|
|
568 This template draws the motif/sequence annotations for each
|
|
|
569 of the scanned sequence less than 10kb.
|
|
|
570 -->
|
|
|
571 <hr/>
|
|
|
572 <center>
|
|
|
573 <big><b><a name="sec_iii">SECTION III: SEQUENCE/MOTIF ANNOTATIONS</a></b></big>
|
|
|
574 </center>
|
|
|
575 <hr/>
|
|
|
576 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[not (@name = preceding::cis:scanned-sequence/@name)]">
|
|
|
577 <xsl:sort select="@name" order="ascending"/>
|
|
|
578 <xsl:variable name="sequence_length" select="@length"/>
|
|
|
579 <xsl:variable name="sequence_name" select="@name"/>
|
|
|
580 <p>
|
|
|
581 <a name="annotation_{$sequence_name}"><xsl:value-of select="$sequence_name"/></a>
|
|
|
582 <br />
|
|
|
583 <span style="background-color: ##DDDD88;"><a href="#occurrences_{$sequence_name}">S</a></span>
|
|
|
584 <span style="background-color: #DDFFDD;"><a href="#diagram_{$sequence_name}">D</a></span>
|
|
|
585 <span style="background-color: #FFFFFF;"><a href="#button_help">?</a></span>
|
|
|
586 </p>
|
|
|
587 <p>
|
|
|
588 Length = <xsl:value-of select="$sequence_length"/>
|
|
|
589 </p>
|
|
|
590 <p>
|
|
|
591 String Length = <xsl:value-of
|
|
|
592 select="string-length(normalize-space(document('matched_sequences.xml')/matched-sequences/sequence[@name=$sequence_name]))"/>
|
|
|
593 </p>
|
|
|
594 <pre>
|
|
|
595 <table style="font-family: monospace;">
|
|
|
596 <tbody>
|
|
|
597 <xsl:call-template name="wrap_sequence">
|
|
|
598 <xsl:with-param name="sequence"
|
|
|
599 select="normalize-space(document('matched_sequences.xml')/matched-sequences/sequence[@name=$sequence_name])"/>
|
|
|
600 <xsl:with-param name="sequence_index" select="1"/>
|
|
|
601 <xsl:with-param name="sequence_name" select="$sequence_name"/>
|
|
|
602 </xsl:call-template>
|
|
|
603 </tbody>
|
|
|
604 </table>
|
|
|
605 </pre>
|
|
|
606 <hr/>
|
|
|
607 </xsl:for-each>
|
|
|
608
|
|
|
609 </xsl:template>
|
|
|
610
|
|
|
611 <xsl:template name="debugging_information">
|
|
|
612 <!-- This template print the HTML describing the FIMO input parameters. -->
|
|
|
613 <hr/>
|
|
|
614 <center>
|
|
|
615 <big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big>
|
|
|
616 </center>
|
|
|
617 <hr/>
|
|
|
618 <p>
|
|
|
619 Command line:
|
|
|
620 </p>
|
|
|
621 <pre>
|
|
|
622 <xsl:value-of select="/fimo/command-line"/>
|
|
|
623 </pre>
|
|
|
624 <p>
|
|
|
625 Settings:
|
|
|
626 </p>
|
|
|
627 <pre>
|
|
|
628 <table>
|
|
|
629 <xsl:apply-templates select="/fimo/settings/setting[position() mod 3 = 1]"/>
|
|
|
630 </table>
|
|
|
631 </pre>
|
|
|
632 <p>
|
|
|
633 This information can be useful in the event you wish to report a
|
|
|
634 problem with the FIMO software.
|
|
|
635 </p>
|
|
|
636 <hr />
|
|
|
637 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
|
|
|
638
|
|
|
639 </xsl:template>
|
|
|
640
|
|
|
641 <xsl:template match="setting">
|
|
|
642 <!-- This template prints the program settings in 2 columns -->
|
|
|
643 <tr>
|
|
|
644 <td style="padding-right: 2em"><xsl:value-of select="@name"/> = <xsl:value-of select="."/></td>
|
|
|
645 <xsl:choose>
|
|
|
646 <xsl:when test="count(following-sibling::*[name()=name(current())])">
|
|
|
647 <td style="padding-left: 5em; padding-right: 2em">
|
|
|
648 <xsl:value-of select="following-sibling::setting[1]/@name"/> = <xsl:value-of select="following-sibling::setting[1]"/>
|
|
|
649 </td>
|
|
|
650 <td style="padding-left: 5em; padding-right: 2em">
|
|
|
651 <xsl:value-of select="following-sibling::setting[2]/@name"/> = <xsl:value-of select="following-sibling::setting[2]"/>
|
|
|
652 </td>
|
|
|
653 </xsl:when>
|
|
|
654 <xsl:otherwise>
|
|
|
655 <td style="padding-left: 5em; padding-right: 2em"></td>
|
|
|
656 <td align="right"></td>
|
|
|
657 </xsl:otherwise>
|
|
|
658 </xsl:choose>
|
|
|
659 </tr>
|
|
|
660 </xsl:template>
|
|
|
661
|
|
|
662 <xsl:template name="button_help">
|
|
|
663 <hr />
|
|
|
664 <center>
|
|
|
665 <h3><a name="button_help">Button Help</a></h3>
|
|
|
666 </center>
|
|
|
667 <hr />
|
|
|
668 <span style="background-color: #DDDDFF">S</span>
|
|
|
669 Links to Entrez database at <a href="http://www.ncbi.nlm.nih.gov">NCBI</a>
|
|
|
670 <span style="background-color: #DDDD88">S</span>
|
|
|
671 Links to motif occurences table(<a href="#sec_i">SECTION I</a>)
|
|
|
672 <br/>
|
|
|
673 <span style="background-color: #DDFFDD">D</span>
|
|
|
674 Links to motif occurences diagram (<a href="#sec_ii">SECTION II</a>)
|
|
|
675 <br />
|
|
|
676 <span style="background-color: #FFDDDD">A</span>
|
|
|
677 Links to sequence/motif annotated alignments (<a href="#sec_iii">SECTION III</a>)
|
|
|
678 <br />
|
|
|
679 <span style="background-color: #FFFFFF">?</span>
|
|
|
680 This information
|
|
|
681 <br />
|
|
|
682
|
|
|
683 <hr />
|
|
|
684 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
|
|
|
685 </xsl:template>
|
|
|
686
|
|
|
687 <xsl:template name="wrap_sequence">
|
|
|
688 <xsl:param name="sequence"/>
|
|
|
689 <xsl:param name="sequence_index"/>
|
|
|
690 <xsl:param name="sequence_name"/>
|
|
|
691 <xsl:variable name="current_sequence">
|
|
|
692 <xsl:value-of select="substring($sequence, 1, 75)"/>
|
|
|
693 </xsl:variable>
|
|
|
694 <tr>
|
|
|
695 <td></td>
|
|
|
696 <td>
|
|
|
697 <xsl:call-template name="annotate_motif_names">
|
|
|
698 <xsl:with-param name="sequence_index" select="$sequence_index"/>
|
|
|
699 <xsl:with-param name="sequence_name" select="$sequence_name"/>
|
|
|
700 <xsl:with-param name="current_sequence" select="$current_sequence" />
|
|
|
701 </xsl:call-template>
|
|
|
702 </td>
|
|
|
703 </tr>
|
|
|
704 <tr>
|
|
|
705 <td style="width: 6em;"><xsl:value-of select ="$sequence_index"/></td>
|
|
|
706 <td><xsl:value-of select="$current_sequence"/></td>
|
|
|
707 </tr>
|
|
|
708 <xsl:variable name="new_sequence" select="substring($sequence, 76)"/>
|
|
|
709 <xsl:if test="string-length($new_sequence)">
|
|
|
710 <xsl:call-template name="wrap_sequence">
|
|
|
711 <xsl:with-param name="sequence" select="$new_sequence"/>
|
|
|
712 <xsl:with-param name="sequence_index" select="number($sequence_index) + 75"/>
|
|
|
713 <xsl:with-param name="sequence_name" select="$sequence_name"/>
|
|
|
714 </xsl:call-template>
|
|
|
715 </xsl:if>
|
|
|
716 </xsl:template>
|
|
|
717
|
|
|
718 <xsl:template name="annotate_motif_names">
|
|
|
719 <xsl:param name="sequence_index"/>
|
|
|
720 <xsl:param name="sequence_name"/>
|
|
|
721 <xsl:param name="input_sequence"/>
|
|
|
722 <xsl:param name="output_sequence"/>
|
|
|
723 <xsl:choose>
|
|
|
724 <xsl:when test="count(document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name=$sequence_name]) = 1">
|
|
|
725 </xsl:when>
|
|
|
726 </xsl:choose>
|
|
|
727 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name=$sequence_name]">
|
|
|
728 <xsl:for-each select="./cis:matched-element[(@start >= $sequence_index) and (@start < ($sequence_index + 75))]">
|
|
|
729 <xsl:sort select="@start" data-type="number" />
|
|
|
730 <xsl:text> </xsl:text><xsl:value-of select="../../@name"/>
|
|
|
731 </xsl:for-each>
|
|
|
732 </xsl:for-each>
|
|
|
733 </xsl:template>
|
|
|
734
|
|
|
735 <xsl:template name="annotate_pvalues">
|
|
|
736 <xsl:param name="sequence_index"/>
|
|
|
737 <xsl:param name="sequence_name"/>
|
|
|
738 <pre>
|
|
|
739 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name=$sequence_name]">
|
|
|
740 <xsl:for-each select="./cis:matched-element[(@start >= $sequence_index) and (@start < ($sequence_index + 75))]">
|
|
|
741 <xsl:sort select="@start" data-type="number" />
|
|
|
742 <xsl:text> </xsl:text><xsl:value-of select="@pvalue"/>
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|
|
743 </xsl:for-each>
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|
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744 </xsl:for-each>
|
|
|
745 </pre>
|
|
|
746 </xsl:template>
|
|
|
747
|
|
|
748 <xsl:template name="annotate_best_match">
|
|
|
749 <xsl:param name="sequence_index"/>
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|
|
750 <xsl:param name="sequence_name"/>
|
|
|
751 <pre>
|
|
|
752 <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name=$sequence_name]">
|
|
|
753 <xsl:for-each select="./cis:matched-element[(@start >= $sequence_index) and (@start < ($sequence_index + 75))]">
|
|
|
754 <xsl:sort select="@start" data-type="number" />
|
|
|
755 <xsl:text> </xsl:text><xsl:value-of select="document('fimo.xml')/fimo/motif[@name=./@name]/@best-possible-match"/>
|
|
|
756 </xsl:for-each>
|
|
|
757 </xsl:for-each>
|
|
|
758 </pre>
|
|
|
759 </xsl:template>
|
|
|
760 </xsl:stylesheet>
|
|
|
761
|
