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author davidmurphy
date Sat, 31 Mar 2012 16:07:07 -0400
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1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
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2 "http://www.w3.org/TR/html4/transitional.dtd">
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3 <html>
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4 <head>
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5 <link rel="stylesheet" type="text/css" href="logo.css" >
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6 <title>CodonLogo - User's Manual</title>
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7 <meta name="author" content="Gavin E. Crooks" >
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8
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9 <style type="text/css">
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10 </style>
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11 </head>
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12
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13 <body style="align:center">
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15 <table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
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16 <tr><td >
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17 <h1>CodonLogo 1.0: User's Manual</h1>
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18
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19 </td><td align = "right" >
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20 &middot;
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21 <a href="./">about</a>&nbsp;&middot;
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22 <a href="create.cgi">create</a>&nbsp;&middot;
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23 <a href="examples.html">examples</a>&nbsp;&middot;
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24 <a class="selected" href="manual.html">manual</a>&nbsp;&middot;
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25 <br>
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26 <span style="font-size:small">&nbsp;</span>&nbsp;&nbsp;
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27
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28 </td></tr>
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29
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30 <tr><td colspan="2" class="discourse">
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31
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32 <h4>Contents</h4>
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33
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34 <img alt="Sequence logo example."
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35 src="img/example.png" align="right" vspace="5" hspace="10">
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36 <!--
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37 <img alt="WebLogo: Create" width="499" height="633"
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38 src="img/weblogo_create.png" align="right" border='1' vspace="10" hspace="10"></a>
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39 -->
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40
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41 <ul>
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42 <li><a href="#intro">Introduction</a>
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43 </li><li><a href="#create">Creating Sequences Logos using the Web interface</a>
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44 </li><li><a href="#download">Downloading and Installing CodonLogo</a>
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45 </li><li><a href="#CLI"> Command Line Interface (CLI)</a>
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46 </li><li><a href="#API"> Application Programmer Interface (API)</a>
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47 </li><li><a href="#dev"> Development and Future Features</a>
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48 </li><li><a href="#misc">Miscellanea</a>
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49 </li>
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50 </ul>
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51
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52
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53 <a name="intro" ></a><h2>Introduction</h2>
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54
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56 <p>
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57 <strong>CodonLogo</strong>
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58 is a web based application designed to make the
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59 <a href="create.cgi">generation</a> of
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60 codon sequence logos as easy and painless as possible.
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61 It is almost entirely based on the application WebLogo.
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62 </p>
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63
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64
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65 <p>
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66 <a href="http://www.lecb.ncifcrf.gov/~toms/sequencelogo.html">Sequence&nbsp;logos</a>
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67 are a graphical representation of an amino acid
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68 or nucleic acid multiple sequence alignment.
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69 Each logo consists of stacks of symbols, one stack for each position in the
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70 sequence. The overall height of the stack indicates the sequence conservation
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71 at that position, while the height of symbols within the stack indicates the
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72 relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position. (Positions with many gasp have thin stacks.) In general, a sequence logo provides a richer and more precise description of, for example,
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73 a binding site, than would a consensus sequence.
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74 </p>
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81
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82 <!-- ============================================================== -->
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83
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84 <h4>References</h4>
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85
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86
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87 <p>
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88 <a href="http://bespoke.lbl.gov/">Crooks GE</a>,
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89 <a href="http://compbio.berkeley.edu/">Hon G</a>,
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90 <a href="http://compbio.berkeley.edu/">Chandonia JM</a>,
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91 <a href="http://compbio.berkeley.edu/people/brenner/">Brenner SE</a>
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92 WebLogo: A sequence logo
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93 generator,
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94 <em>Genome Research</em>, 14:1188-1190, (2004)
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95 [<a href="http://bespoke.lbl.gov/pubs/fulltext/Crooks2004a-GR-WebLogo.pdf">Full Text</a> ]
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96 </p>
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97
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98 <p>
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99 Schneider TD, Stephens RM. 1990.
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100 <a class="out" href="http://www.lecb.ncifcrf.gov/~toms/paper/logopaper/">Sequence Logos: A New Way to Display Consensus Sequences.</a>
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101 <em>Nucleic Acids Res.</em> <em>18</em>:6097-6100
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102 </p>
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103
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104
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105
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106
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107
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108
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109
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110 <a name="create" ></a>
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111 <h2>Creating Sequences Logos using the Web interface</h2>
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112
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113
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114 <h4>Sequence Data</h4>
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115 Enter your multiple sequence alignment here, or select a file to upload. Supported file formats include CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP. All sequences must be the same length, else CodonLogo will return an error and report the first sequence that differed in length from previous sequences.
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116
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117 <h4>Output format</h4>
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118
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119 <ul>
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120 <li> PNG : (600 DPI) Print resolution bitmap
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121 </li><li> PNG : (low res, 96 DPI) Screen resolution bitmap
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122 </li><li> JPEG :Screen resolution bitmap
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123 </li><li> EPS : Encapsulated postscript
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124 </li><li> PDF : Portable Document Format
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125 </li>
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126 </ul>
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127 Generally speaking, vector formats (EPS and PDF) are better for printing, while bitmaps (JPEG and PNG) are more suitable for displaying on the screen or embedding into a web page.
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128
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129 <h4>Logo size</h4>
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130 The physical dimensions of the generated logo.
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131 Specifically, controls the size of individual symbols stacks.
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132 <ul>
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133 <li> small : 5.4 points wide (Same as 9pt Courier), aspect ratio 5:1
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134 </li><li> medium : Double the width and height of small.
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135 </li><li> large : Triple the width and height of small.
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136 </li>
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137 </ul>
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138 The choices have been limited to promote inter-logo consistency. Small logos can fit 80 stacks across a printed page, or 40 across a half page column. The <a href="#CLI">command line interface</a> provides greater control, if so desired.
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139
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140 <h4>Stacks per line</h4>
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141 If the length of the sequences is greater than this maximum number of stacks per line, then the logo will be split across multiple lines.
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142
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143 <h4>Sequence type</h4>
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144 The type of biological molecule.
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145 <ul>
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146 <li> auto: Automatically guess sequence type from the data
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147 </li><li> protein
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148 </li><li> dna
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149 </li><li> rna
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150 </li>
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151 </ul>
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152
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153 <h4>Ignore lower case</h4>
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154 Disregard lower case letters in the and only count
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155 upper case letters in sequences?
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156
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157 <h4>Units</h4>
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158 The units used for the y-axis.
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159 <ul>
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160 <li> probability: Show residue probabilities, rather than information content. If <a href="#CA">compositional adjustment</a> is disabled, then these are the raw residue frequencies.
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161 </li><li> bits: Information content in bits
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162 </li><li> nats: Natural units, 1 bit = ln 2 (0.69) nats
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163 </li><li> kT : Thermal energy units in natural units (Numerically the same as nats)
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164 </li><li> kJ/mol : Thermal energy (Assuming T = 300 K)
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165 </li><li> kcal/mol : Thermal energy (Assuming T = 300 K)
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166 </li>
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167 </ul>
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168
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169
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170 <h4>First position number</h4>
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171 The numerical label of the first residue in the multiple sequence alignment. The label must be an integer. Residue labels for the logo will be relative to this number. (See also: Logo Range)
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172 <h4>Logo range</h4>
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173 By default, all sequence data is displayed in the Sequence Logo. With this option, you can instead show a subrange of the entire sequence. Start and end positions are included, and the numbering of positions is relative to the sequence number of the first position. (See also: First Position Number ) Thus, if the first position number is "2", start is "5" and end is "10", then the 4th through 9th (inclusive) sequence positions will be displayed, and they will be numbered "5", "6", "7", "8", "9" and "10".
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174
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175 <a name="CA"></a>
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176 <h4>Composition</h4>
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177 <p>
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178 The background composition of the genome or proteome from which the sequences have been drawn. The default, automatic option is to use equiprobable background for nucleic acids and a typical amino acid usage pattern for proteins. However, you may also explicitly set the expected CG content for nucleic acid sequences, insists on equiprobable background distributions, or turn off composition adjustment altogether.
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179 </p>
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180 <p>
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181 Compositional adjustment has two effects. First, the information content of a site is defined as the relative entropy of the monomers at that site to the background distribution. Consequentially, rare monomers have higher information content (when they occur) than relatively common monomers.
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182 </p>
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183 <p>
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184 Secondly, the background composition is used in the small sample correction of information content. Briefly, if only a few sequences are available in the multiple sequence alignment, then sites typically appear more conserved than they really are. Small samples bias the relative entropy upwards. To compensate, we add pseudocounts to the actual counts, proportional to the expected background composition. These pseudocounts smooth the data for small samples, but become irrelevant for large samples. The proportionality constant is set to 4 for nucleic acid sequences, and 20 for proteins (These numbers have been found to give reasonable results in practice).
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185 </p>
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186 <p>
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187 Behind the scenes, things are more complex. We do a full Bayesian calculation, starting with explicit Dirichlet priors based on the background composition, to which we add the data and then calculate both the posterior mean relative entropy (the stack height) and Bayesian 95% confidence intervals for error bars. These interesting details will be explained elsewhere.
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188 </p>
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189
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190 <h4>Scale stack width</h4>
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191 Scale the visible stack width by the fraction of symbols in the column? (i.e. columns with many gaps or unknown residues are narrow.)
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192
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193 <h4>Error bars</h4>
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194 Display error bars. These indicate an approximate, Bayesian 95% confidence interval.
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195
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196 <h4>Title</h4>
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197 Give your logo a title.
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198
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199 <h4>Figure label</h4>
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200 An optional figure label, added to the top left (e.g. '(a)')
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201
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202 <h4>X-axis</h4>
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203 Add a label to the x-axis, or hide axis altogether.
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204
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205 <h4>Y-axis</h4>
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206 The vertical axis indicates the information content of a sequence position. Use this option to toggle the y-axis and override the default axis label.
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207
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208 <h4>Y-axis scale</h4>
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209 The height of the y-axis in designated units. The automatic option will pick reasonable defaults based on the sequence type and axis unit.
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210
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211 <h4>Y-axis tic spacing</h4>
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212 The distance between major tic marks on the Y-axis.
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213
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214 <h4>Sequence end labels</h4>
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215 Choose this option to label the 5' &amp; 3' ends of nucleic acid or the N &amp; C termini of amino acid sequences.
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216
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217 <h4>Version fineprint</h4>
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218 Toggle display of the CodonLogo version information in the lower right corner.
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219
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220 <h4>Color Scheme</h4>
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221 <ul>
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222 <li> auto : use Base Pairing for nucleic acids (NA), Hydrophobicity for amino acids (AA).
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223 </li><li> monochrome: All symbols black
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224 </li><li> Base Pairing (NA default) :
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225 <table border="1" cellpadding="2" cellspacing="0" >
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226 <tr><td>2 Watson-Crick hydrogen bonds</td><td>TAU</td><td style="color:darkorange">dark orange</td></tr>
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227 <tr><td>3 Watson-Crick hydrogen bonds</td><td>GC</td><td style="color:blue"> blue</td></tr>
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228 </table>
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229
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230 </li><li> Classic (NA) : WebLogo (version 1 and 2) and makelogo default color scheme for nucleic acids: G, orange; T &amp; U, red; C, blue; and A, green.
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231 <table border="1" cellpadding="2" cellspacing="0" >
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232 <tr><td>G</td><td style="color:orange"> orange</td></tr>
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233 <tr><td>TU</td><td style="color:red"> red</td></tr>
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234 <tr><td>C</td><td style="color:blue">blue</td></tr>
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235 <tr><td>A</td><td style="color:green">green</td></tr>
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236 </table>
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237
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238 </li><li> Hydrophobicity (AA default) :
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239 <table border="1" cellpadding="2" cellspacing="0" >
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240 <tr><td>Hydrophobic</td><td>RKDENQ</td><td style="color:black"> black</td></tr>
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241 <tr><td>Neutral</td><td>SGHTAP</td><td style="color:green"> green</td></tr>
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242 <tr><td>Hydrophilic</td><td>YVMCLFIW</td><td style="color:blue">blue</td></tr>
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243 </table>
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244
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245 </li><li> Chemistry (AA): Color amino acids according to chemical properties. WebLogo (version 1 and 2) and makelogo default color.
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246 <table border="1" cellpadding="2" cellspacing="0" >
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247 <tr><td>Polar</td><td>G,S,T,Y,C,Q,N</td><td style="color:green"> green</td></tr>
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248 <tr><td>Basic</td><td>K,R,H</td><td style="color:blue"> blue</td></tr>
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249 <tr><td>Acidic</td><td>D,E</td><td style="color:red">red</td></tr>
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250 <tr><td>Hydrophobic</td><td>A,V,L,I,P,W,F,M</td><td style="color:black">black</td></tr>
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251 </table>
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252
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253 </li><li> Charge (AA) :
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254 <table border="1" cellpadding="2" cellspacing="0" >
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255 <tr><td>Positive</td><td>KRH</td><td style="color:blue"> blue</td></tr>
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256 <tr><td>Negative</td><td>DE</td><td style="color:red"> red</td></tr>
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257 </table>
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258
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259
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260
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261
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262 </li><li> Custom : A custom color scheme can be specified in the input field below. Specify colors on the left and associated symbols on the right. Colors are entered using <a href="http://www.w3.org/TR/REC-CSS2/syndata.html#color-units">CSS2 (Cascading Style Sheet)</a> syntax. (e.g. 'red', '#F00', '#FF0000', 'rgb(255, 0, 0)', 'rgb(100%, 0%, 0%)' or 'hsl(0, 100%, 50%)' for the color red.)
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263 </li>
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264 </ul>
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265
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266 <h4>More Options</h4>
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267 The CodonLogo <a href="#CLI">command line client</a>, <code>codonlogo</code>, provides many more options and greater control over the final logo appearance.
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268
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269
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270
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271
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272
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273
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davidmurphy
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274 <!-- ========================================================= -->
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275 <a name="download" ></a>
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276 <h2>Installing CodonLogo</h2>
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277
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278
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279 <h4>Dependencies</h4>
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280 <p>
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281 CodonLogo is written in python. It is necessary to have <a href="http://www.python.org/download/">python 2.3, 2.4 or 2.5</a> and the
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282 extension packages <a href="http://www.scipy.org/Download">numpy</a> and
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283 <a href="http://code.google.com/p/corebio">corebio</a>
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284 installed before WebLogo will run. WebLogo also requires a recent version of <a href="http://www.cs.wisc.edu/~ghost/">ghostscript</a> to create PNG and PDF output.
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285 </p>
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286
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287 <!--
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davidmurphy
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288 <h4> Download and Installation</h4>
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289 <p>
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290 If the python package <a href="http://peak.telecommunity.com/DevCenter/setuptools"><code>setuptools</code></a> has been installed, then WebLogo and its dependancies can be downloaded and installed with a single command:
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291 <pre>
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292 sudo easy_install weblogo
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davidmurphy
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293 </pre>
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davidmurphy
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294 </p>-->
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davidmurphy
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295 <!--
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davidmurphy
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296 <p>
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davidmurphy
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297 Alternatively, CodonLogo and its dependancies can be installed manually.
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davidmurphy
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298 The CodonLogo source code can be downloaded from
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299 <a href="http://code.google.com/p/weblogo/">http://code.google.com/p/weblogo/</a>.
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300 This code is distributed under various <a href="http://www.opensource.org/docs/definition">open source licenses</a>. Please consult the <code>LICENSE.txt</code> file in the source distribution for details.
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301 </p>-->
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302
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davidmurphy
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303 <p>
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304 After unpacking the CodonLogo tarfile, it should be possible to immediately create
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305 logos using the command line client (Provided that python, numpy, corebio and ghostscript have already been installed).
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davidmurphy
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306 </p>
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davidmurphy
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307 <pre>
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308 ./codonlogo --format PNG &lt; htdocs/examples/cap_hth.fa &gt; cap_hth.png
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davidmurphy
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309 </pre>
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davidmurphy
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310 <p>
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311 Please consult the file <code>build_examples.sh</code> for more examples.
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312 </p><p>
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313 To run CodonLogo as a stand alone web service, run the logo server command :
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davidmurphy
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314 </p>
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davidmurphy
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315 <pre>
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davidmurphy
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316 ./codonlogo --serve
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davidmurphy
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317 </pre>
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davidmurphy
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318 <p>
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319 It should now be possible to access CodonLogo at <a href="http://localhost:8080/">http://localhost:8080/</a>.
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320 </p>
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davidmurphy
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321
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322 <p>
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323 The command line client and WebLogo libraries can be permanently installed using the supplied <code>setup.py</code> script.
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324 <pre>
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325 sudo python setup.py install
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davidmurphy
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326 </pre>
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327 Run <code>python setup.py help</code> for more installation options. For example, to specifically install the CodonLogo script to /usr/local/bin
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328 <pre>
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329 sudo python setup.py install_scripts --install-dir /usr/local/bin
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davidmurphy
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330 </pre>
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davidmurphy
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331 </p>
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davidmurphy
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332
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333
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334 </p>
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335 <h4>Web App</h4>
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336
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337 <p>
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338 To use CodonLogo as a web application, first install the weblogo dependancies and libraries as above, then
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339 place (or link) the <code>weblogolib/weblogo_htdocs</code> directory
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340 somewhere within the document root of your webserver. The webserver
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341 must be able to execute the CGI script <code>create.cgi</code>. For Apache, you may have to add an <code>ExecCGI</code>
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342 option and add a cgi handler in the <code>httpd.conf</code> configuration file.
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davidmurphy
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343 Something like this:
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344 </p>
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davidmurphy
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345 <pre>
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davidmurphy
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346 &lt;Directory "/home/httpd/htdocs/weblogo/">
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347 Options FollowSymLinks MultiViews ExecCGI
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348 AllowOverride None
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davidmurphy
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349 Order allow,deny
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davidmurphy
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350 Allow from all
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davidmurphy
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351 &lt;/Directory>
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352 ...
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353 # To use CGI scripts outside of ScriptAliased directories:
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354 # (You will also need to add "ExecCGI" to the "Options" directive.)
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355 #
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356 AddHandler cgi-script .cgi
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357 </pre>
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358 It may also be necessary to set the <code>PATH</code> and <code>PYTHONPATH</code> environment variables.
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359 <pre>
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360 SetEnv PYTHONPATH /path/to/weblogo/libraries
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361 </pre>
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362 The cgi script also has to be able to find the '<code>gs</code>' ghostscript executable. If ghostscipt is installed in a non-standard location add the following environment variable.
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363 <pre>
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364 SetEnv COREBIOPATH /path/to/gs
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365 </pre>
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366 The maxium bytes of uploaded sequecne data can be controlled with the <code>WEBLOGO_MAX_FILE_SIZE</code> environment variable.
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367 <pre>
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368 SetEnv WEBLOGO_MAX_FILE_SIZE 1000000
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369 </pre>
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370
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371
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372
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373
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374 <!-- ================================================================== -->
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375 <a name="CLI" ></a>
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diff changeset
376 <h2><code>codonlogo</code>, The CodonLogo Command Line Interface (CLI)</h2>
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davidmurphy
parents:
diff changeset
377 The command line client has many options not available through the web interface. Please consult the bundled <code>build_examples.sh</code> script for inspiration.
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davidmurphy
parents:
diff changeset
378 <pre >
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davidmurphy
parents:
diff changeset
379 Usage: codonlogo [options] < sequence_data.fa > sequence_logo.eps
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davidmurphy
parents:
diff changeset
380
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davidmurphy
parents:
diff changeset
381 Create sequence logos from biological sequence alignments.
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davidmurphy
parents:
diff changeset
382
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davidmurphy
parents:
diff changeset
383 Options:
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davidmurphy
parents:
diff changeset
384 --version show program's version number and exit
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davidmurphy
parents:
diff changeset
385 -h --help show this help message and exit
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davidmurphy
parents:
diff changeset
386
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davidmurphy
parents:
diff changeset
387 Input/Output Options:
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davidmurphy
parents:
diff changeset
388 -f --fin FILENAME Sequence input file (default: stdin)
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davidmurphy
parents:
diff changeset
389 --fin-format FORMAT Multiple sequence alignment format: (clustal,
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davidmurphy
parents:
diff changeset
390 fasta, plain, msf, genbank, nbrf, nexus,
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davidmurphy
parents:
diff changeset
391 phylip, stockholm, intelligenetics, table,
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davidmurphy
parents:
diff changeset
392 array)
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davidmurphy
parents:
diff changeset
393 -o --fout FILENAME Output file (default: stdout)
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davidmurphy
parents:
diff changeset
394 -F --format FORMAT Format of output: eps (default), png,
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davidmurphy
parents:
diff changeset
395 png_print, pdf, jpeg, txt
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davidmurphy
parents:
diff changeset
396
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davidmurphy
parents:
diff changeset
397 Logo Data Options:
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davidmurphy
parents:
diff changeset
398 -A --sequence-type TYPE The type of sequence data: 'protein', 'rna' or
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davidmurphy
parents:
diff changeset
399 'dna'.
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davidmurphy
parents:
diff changeset
400 -a --alphabet ALPHABET The set of symbols to count, e.g. 'AGTC'. All
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davidmurphy
parents:
diff changeset
401 characters not in the alphabet are ignored. If
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davidmurphy
parents:
diff changeset
402 neither the alphabet nor sequence-type are
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davidmurphy
parents:
diff changeset
403 specified then weblogo will examine the input
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davidmurphy
parents:
diff changeset
404 data and make an educated guess. See also
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davidmurphy
parents:
diff changeset
405 --sequence-type, --ignore-lower-case
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davidmurphy
parents:
diff changeset
406 --ignore-lower-case YES/NO
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davidmurphy
parents:
diff changeset
407 Disregard lower case letters and only count
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davidmurphy
parents:
diff changeset
408 upper case letters in sequences? (Default: No)
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davidmurphy
parents:
diff changeset
409 -U --units NUMBER A unit of entropy ('bits' (default), 'nats',
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davidmurphy
parents:
diff changeset
410 'digits'), or a unit of free energy ('kT',
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davidmurphy
parents:
diff changeset
411 'kJ/mol', 'kcal/mol'), or 'probability' for
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davidmurphy
parents:
diff changeset
412 probabilities
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davidmurphy
parents:
diff changeset
413 --composition COMP. The expected composition of the sequences:
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davidmurphy
parents:
diff changeset
414 'auto' (default), 'equiprobable', 'none' (Do
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davidmurphy
parents:
diff changeset
415 not perform any compositional adjustment), a
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davidmurphy
parents:
diff changeset
416 CG percentage, a species name (e.g. 'E. coli',
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davidmurphy
parents:
diff changeset
417 'H. sapiens'), or an explicit distribution
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davidmurphy
parents:
diff changeset
418 (e.g. {'A':10, 'C':40, 'G':40, 'T':10}). The
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davidmurphy
parents:
diff changeset
419 automatic option uses a typical distribution
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davidmurphy
parents:
diff changeset
420 for proteins and equiprobable distribution for
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davidmurphy
parents:
diff changeset
421 everything else.
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davidmurphy
parents:
diff changeset
422 --weight NUMBER The weight of prior data. Default: total
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davidmurphy
parents:
diff changeset
423 pseudocounts equal to the number of monomer
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davidmurphy
parents:
diff changeset
424 types.
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davidmurphy
parents:
diff changeset
425 -i --first-index INDEX Index of first position in sequence data
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davidmurphy
parents:
diff changeset
426 (default: 1)
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davidmurphy
parents:
diff changeset
427 -l --lower INDEX Lower bound of sequence to display
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davidmurphy
parents:
diff changeset
428 -u --upper INDEX Upper bound of sequence to display
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davidmurphy
parents:
diff changeset
429
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davidmurphy
parents:
diff changeset
430 Logo Format Options:
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davidmurphy
parents:
diff changeset
431 These options control the format and display of the logo.
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davidmurphy
parents:
diff changeset
432
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davidmurphy
parents:
diff changeset
433 -s --size LOGOSIZE Specify a standard logo size (small, medium
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davidmurphy
parents:
diff changeset
434 (default), large)
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davidmurphy
parents:
diff changeset
435 -n --stacks-per-line COUNT Maximum number of logo stacks per logo line.
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davidmurphy
parents:
diff changeset
436 (default: 40)
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davidmurphy
parents:
diff changeset
437 -t --title TEXT Logo title text.
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davidmurphy
parents:
diff changeset
438 --label TEXT A figure label, e.g. '2a'
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davidmurphy
parents:
diff changeset
439 -X --show-xaxis YES/NO Display sequence numbers along x-axis?
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davidmurphy
parents:
diff changeset
440 (default: True)
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davidmurphy
parents:
diff changeset
441 -x --xlabel TEXT X-axis label
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davidmurphy
parents:
diff changeset
442 -S --yaxis UNIT Height of yaxis in units. (Default: Maximum
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davidmurphy
parents:
diff changeset
443 value with uninformative prior.)
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davidmurphy
parents:
diff changeset
444 -Y --show-yaxis YES/NO Display entropy scale along y-axis? (default:
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davidmurphy
parents:
diff changeset
445 True)
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davidmurphy
parents:
diff changeset
446 -y --ylabel TEXT Y-axis label (default depends on plot type
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davidmurphy
parents:
diff changeset
447 and units)
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davidmurphy
parents:
diff changeset
448 -E --show-ends YES/NO Label the ends of the sequence? (default:
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davidmurphy
parents:
diff changeset
449 False)
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davidmurphy
parents:
diff changeset
450 -P --fineprint TEXT The fine print (default: weblogo version)
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davidmurphy
parents:
diff changeset
451 --ticmarks NUMBER Distance between ticmarks (default: 1.0)
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davidmurphy
parents:
diff changeset
452 --errorbars YES/NO Display error bars? (default: True)
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davidmurphy
parents:
diff changeset
453
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davidmurphy
parents:
diff changeset
454 Color Options:
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davidmurphy
parents:
diff changeset
455 Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc.
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davidmurphy
parents:
diff changeset
456
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davidmurphy
parents:
diff changeset
457 -c --color-scheme SCHEME Specify a standard color scheme (auto, base
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davidmurphy
parents:
diff changeset
458 pairing, charge, chemistry, classic,
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davidmurphy
parents:
diff changeset
459 hydrophobicity, monochrome)
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davidmurphy
parents:
diff changeset
460 -C --color COLOR SYMBOLS DESCRIPTION
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davidmurphy
parents:
diff changeset
461 Specify symbol colors, e.g. --color black AG
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davidmurphy
parents:
diff changeset
462 'Purine' --color red TC 'Pyrimidine'
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davidmurphy
parents:
diff changeset
463 --default-color COLOR Symbol color if not otherwise specified.
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davidmurphy
parents:
diff changeset
464
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davidmurphy
parents:
diff changeset
465 Advanced Format Options:
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davidmurphy
parents:
diff changeset
466 These options provide fine control over the display of the logo.
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davidmurphy
parents:
diff changeset
467
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davidmurphy
parents:
diff changeset
468 -W --stack-width POINTS Width of a logo stack (default: 10.8)
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davidmurphy
parents:
diff changeset
469 -H --stack-height POINTS Height of a logo stack (default: 54.0)
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davidmurphy
parents:
diff changeset
470 --box YES/NO Draw boxes around symbols? (default: no)
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davidmurphy
parents:
diff changeset
471 --resolution DPI Bitmap resolution in dots per inch (DPI).
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davidmurphy
parents:
diff changeset
472 (default: 96 DPI, except png_print, 600 DPI)
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davidmurphy
parents:
diff changeset
473 Low resolution bitmaps (DPI<300) are
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davidmurphy
parents:
diff changeset
474 antialiased.
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davidmurphy
parents:
diff changeset
475 --scale-width YES/NO Scale the visible stack width by the fraction
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davidmurphy
parents:
diff changeset
476 of symbols in the column? (i.e. columns with
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davidmurphy
parents:
diff changeset
477 many gaps of unknowns are narrow.) (default:
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davidmurphy
parents:
diff changeset
478 yes)
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davidmurphy
parents:
diff changeset
479 --debug YES/NO Output additional diagnostic information.
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davidmurphy
parents:
diff changeset
480 (default: False)
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davidmurphy
parents:
diff changeset
481
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davidmurphy
parents:
diff changeset
482 CodonLogo Server:
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davidmurphy
parents:
diff changeset
483 Run a standalone webserver on a local port.
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davidmurphy
parents:
diff changeset
484
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davidmurphy
parents:
diff changeset
485 --serve Start a standalone CodonLogo server for creating
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davidmurphy
parents:
diff changeset
486 sequence logos.
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davidmurphy
parents:
diff changeset
487 --port PORT Listen to this local port. (Default: 8080)
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davidmurphy
parents:
diff changeset
488 </pre >
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davidmurphy
parents:
diff changeset
489 <!-- ===================================================================== -->
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davidmurphy
parents:
diff changeset
490 <a name="API" ></a>
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davidmurphy
parents:
diff changeset
491 <h2>WebLogo Application Programmer Interface (API)</h2>
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davidmurphy
parents:
diff changeset
492
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davidmurphy
parents:
diff changeset
493 The WebLogo python libraries provide even greater flexibility than the command line client. The code is split between two principle packages, <code>weblogo</code> itself, which contains specialized sequence logo generation code, and <code>corebio</code>, a package that contains code of more general utility.
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davidmurphy
parents:
diff changeset
494 Please consult the <a href="http://weblogo.googlecode.com/svn/trunk/apidocs/index.html">WebLogo</a> and <a href="http://corebio.googlecode.com/svn/tags/0.5.0/apidocs/index.html">CoreBio</a> API documentation.
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davidmurphy
parents:
diff changeset
495
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
496
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
497
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davidmurphy
parents:
diff changeset
498 <!-- ================================================================== -->
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davidmurphy
parents:
diff changeset
499 <a name="dev" ></a>
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davidmurphy
parents:
diff changeset
500 <h2>WebLogo Development and Future Features</h2>
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davidmurphy
parents:
diff changeset
501 <p>
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davidmurphy
parents:
diff changeset
502 The development project is hosted at
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
503 <a href="http://code.google.com/p/weblogo/">http://code.google.com/p/weblogo</a>.
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davidmurphy
parents:
diff changeset
504
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davidmurphy
parents:
diff changeset
505 If you wish to extend WebLogo or to contribute code, then you should download the full source code development package directly from the subversion repository.
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davidmurphy
parents:
diff changeset
506 </p>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
507 <pre>
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davidmurphy
parents:
diff changeset
508 &gt; svn checkout http://weblogo.googlecode.com/svn/trunk/ weblogo
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davidmurphy
parents:
diff changeset
509 &gt; cd weblogo
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davidmurphy
parents:
diff changeset
510 &gt; ./weblogo &lt; cap.fa &gt; cap.eps
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davidmurphy
parents:
diff changeset
511 </pre>
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davidmurphy
parents:
diff changeset
512 <p>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
513 Please consult the developer notes, <code>DEVELOPERS.txt</code> and software license <code>LICENSE.txt</code>
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davidmurphy
parents:
diff changeset
514 </p>
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davidmurphy
parents:
diff changeset
515
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davidmurphy
parents:
diff changeset
516 <p> Outstanding bugs and feature requests are listed on the <a href="http://code.google.com/p/weblogo/issues/list">WebLogo issue tracker.</a>
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davidmurphy
parents:
diff changeset
517 </p>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
518
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davidmurphy
parents:
diff changeset
519 <a name="misc" ></a>
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davidmurphy
parents:
diff changeset
520 <h2>Miscellanea</h2>
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davidmurphy
parents:
diff changeset
521 <h4> Release Notes and Known Bugs</h4>
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davidmurphy
parents:
diff changeset
522 The <a href="weblogo_changelog.txt">WebLogo release notes</a> detail changes to WebLogo and known issues with particular versions.
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davidmurphy
parents:
diff changeset
523
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davidmurphy
parents:
diff changeset
524 <h4>WebLogo 2</h4>
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davidmurphy
parents:
diff changeset
525 The legacy WebLogo 2 sever can be found <a href="http://weblogo.berkeley.edu/">here.</a>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
526
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
527
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
528
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
529 <h4>Acknowledgments</h4>
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davidmurphy
parents:
diff changeset
530
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
531 <p>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
532 WebLogo was created by
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
533 <a href="http://threeplusone.com/">Gavin E. Crooks</a>,
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
534 <a href="http://compbio.berkeley.edu/">Liana Lareau</a>,
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
535 <a href="http://compbio.berkeley.edu/">Gary Hon</a>,
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
536 <a href="http://compbio.berkeley.edu/">John-Marc Chandonia</a> and
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
537 <a href="http://compbio.berkeley.edu/people/brenner/">Steven E. Brenner</a>.
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davidmurphy
parents:
diff changeset
538 <a href="weblogo_changelog.txt">Many others</a> have provided suggestions, bug fixes and moral support.
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
539 </p>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
540
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
541 <p>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
542 WebLogo was originally based upon the programs
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
543 <a href="http://www.lecb.ncifcrf.gov/~toms/delila/alpro.html">alpro</a> and
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
544 <a href="http://www.lecb.ncifcrf.gov/~toms/delila/makelogo.html">makelogo</a>,
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davidmurphy
parents:
diff changeset
545 both of which are part of Tom Schneider's
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
546 <a href="http://www.lecb.ncifcrf.gov/~toms/delila.html">delila</a> package. Many thanks
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davidmurphy
parents:
diff changeset
547 are due to him for making this software freely available and for encouraging its use.
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
548 </p>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
549
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
550
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
551
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
552
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
553
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
554 </td></tr>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
555 </table>
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
556
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
557
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davidmurphy
parents:
diff changeset
558 <script type="text/javascript">
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davidmurphy
parents:
diff changeset
559 var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
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davidmurphy
parents:
diff changeset
560 document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
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davidmurphy
parents:
diff changeset
561 </script>
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davidmurphy
parents:
diff changeset
562 <script type="text/javascript">
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davidmurphy
parents:
diff changeset
563 var pageTracker = _gat._getTracker("UA-5951066-1");
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davidmurphy
parents:
diff changeset
564 pageTracker._trackPageview();
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davidmurphy
parents:
diff changeset
565 </script>
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davidmurphy
parents:
diff changeset
566 </body>
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davidmurphy
parents:
diff changeset
567 </html>
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davidmurphy
parents:
diff changeset
568
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
569
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davidmurphy
parents:
diff changeset
570
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
571
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
572
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
573
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
574
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
575
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
576