Borrelia codon usage: Difference between revisions
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imported>Rayrah (→Data) |
imported>Rayrah (→Charts) |
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==Data== | ==Data== | ||
<h1 | <h1>Report for BBA15</h1> | ||
<p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.47</p> | <p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.47</p> | ||
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<p><a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.</p><h1> | <p><a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.</p><h1>Report for BBA24</h1> | ||
<p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.50</p> | <p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.50</p> | ||
| Line 61: | Line 58: | ||
<p><a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.</p><h1 | <p><a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.</p><h1>Report for BBA68</h1> | ||
<p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.48</p> | <p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.48</p> | ||
| Line 91: | Line 86: | ||
<p><a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.</p><h1> | <p><a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.</p><h1>Report for BBB18</h1> | ||
<p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.50</p> | <p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.50</p> | ||
| Line 119: | Line 113: | ||
<table><tr><td><span style="color:red" cite="http://">A</span></td><td>626</td></tr><tr><td><span style="color:red" cite="http://">T</span></td><td>496</td></tr><tr><td><span style="color:red" cite="http://">G</span></td><td>248</td></tr><tr><td><span style="color:red" cite="http://">C</span></td><td>214</td></tr></table> | <table><tr><td><span style="color:red" cite="http://">A</span></td><td>626</td></tr><tr><td><span style="color:red" cite="http://">T</span></td><td>496</td></tr><tr><td><span style="color:red" cite="http://">G</span></td><td>248</td></tr><tr><td><span style="color:red" cite="http://">C</span></td><td>214</td></tr></table> | ||
<p><a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.</p> | |||
</p><h1>Report for Whole Genome</h1> | |||
<p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.57</p> | |||
<p><span style="color:red" cite="http://">GC percentage for sequence</span> : 28.86%</p> | |||
<p><span style="color:red" cite="http://"><span class="caps">GENETIC CODE USED</span></span> : 1 <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi"><small>more about genetic code</small></a></p> | |||
<p><span style="background:#336699;color:white;padding:5px" cite="http://"><big><b><span class="caps">CODON USAGE</span></b></big></span></p> | |||
<table><tr><td><span style="color:red" cite="http://"><span class="caps">CODON</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCC</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCA</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCG</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">AAC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">AAT</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">GAC</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">GAT</span></span></td><td><span style="background:#99CC99" cite="http://"><span class="caps">TGC</span></span></td><td><span style="background:#99CC99" cite="http://"><span class="caps">TGT</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">CAA</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">CAG</span></span></td><td><span style="background:#FF00CC" cite="http://"><span class="caps">GAG</span></span></td><td><span style="background:#FF00CC" cite="http://"><span class="caps">GAA</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGA</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGT</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGG</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGC</span></span></td><td><span style="background:#66CCFF" cite="http://"><span class="caps">CAC</span></span></td><td><span style="background:#66CCFF" cite="http://"><span class="caps">CAT</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATT</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATC</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTT</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTG</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">TTA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTC</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">TTG</span></span></td><td><span style="background:#FFFFCC" cite="http://"><span class="caps">AAG</span></span></td><td><span style="background:#FFFFCC" cite="http://"><span class="caps">AAA</span></span></td><td><span style="background:#FFFF66" cite="http://"><span class="caps">ATG</span></span></td><td><span style="background:#FFCC00" cite="http://"><span class="caps">TTT</span></span></td><td><span style="background:#FFCC00" cite="http://"><span class="caps">TTC</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCG</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCC</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCA</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGC</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCC</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCT</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TAG</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TGA</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TAA</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACT</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACA</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACG</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">TGG</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">TAT</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">TAC</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTC</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTG</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTT</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTA</span></span></td></tr><tr><td><span style="color:red" cite="http://"><span class="caps">AMINOACID</span></span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#CC99CC" cite="http://">Asn</span></td><td><span style="background:#CC99CC" cite="http://">Asn</span></td><td><span style="background:#99FFCC" cite="http://">Asp</span></td><td><span style="background:#99FFCC" cite="http://">Asp</span></td><td><span style="background:#99CC99" cite="http://">Cys</span></td><td><span style="background:#99CC99" cite="http://">Cys</span></td><td><span style="background:#CCFF00" cite="http://">Gln</span></td><td><span style="background:#CCFF00" cite="http://">Gln</span></td><td><span style="background:#FF00CC" cite="http://">Glu</span></td><td><span style="background:#FF00CC" cite="http://">Glu</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#66CCFF" cite="http://">His</span></td><td><span style="background:#66CCFF" cite="http://">His</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#FFFFCC" cite="http://">Lys</span></td><td><span style="background:#FFFFCC" cite="http://">Lys</span></td><td><span style="background:#FFFF66" cite="http://">Met</span></td><td><span style="background:#FFCC00" cite="http://">Phe</span></td><td><span style="background:#FFCC00" cite="http://">Phe</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#99FFCC" cite="http://">Trp</span></td><td><span style="background:#CCFF00" cite="http://">Tyr</span></td><td><span style="background:#CCFF00" cite="http://">Tyr</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td></tr><tr><td><span style="color:red" cite="http://"><span class="caps">COUNT</span></span></td><td><span style="background:#f4f4f4" cite="http://">2000</span></td><td><span style="background:#f4f4f4" cite="http://">7080</span></td><td><span style="background:#f4f4f4" cite="http://">1187</span></td><td><span style="background:#f4f4f4" cite="http://">8110</span></td><td><span style="background:#FF99FF" cite="http://">1277</span></td><td><span style="background:#FF99FF" cite="http://">3427</span></td><td><span style="background:#FF99FF" cite="http://">913</span></td><td><span style="background:#FF99FF" cite="http://">512</span></td><td><span style="background:#FF99FF" cite="http://">11465</span></td><td><span style="background:#FF99FF" cite="http://">584</span></td><td><span style="background:#CC99CC" cite="http://">6857</span></td><td><span style="background:#CC99CC" cite="http://">25195</span></td><td><span style="background:#99FFCC" cite="http://">3762</span></td><td><span style="background:#99FFCC" cite="http://">15623</span></td><td><span style="background:#99CC99" cite="http://">2397</span></td><td><span style="background:#99CC99" cite="http://">3330</span></td><td><span style="background:#CCFF00" cite="http://">9874</span></td><td><span style="background:#CCFF00" cite="http://">2224</span></td><td><span style="background:#FF00CC" cite="http://">6834</span></td><td><span style="background:#FF00CC" cite="http://">19297</span></td><td><span style="background:#33FFCC" cite="http://">8360</span></td><td><span style="background:#33FFCC" cite="http://">5151</span></td><td><span style="background:#33FFCC" cite="http://">3452</span></td><td><span style="background:#33FFCC" cite="http://">3285</span></td><td><span style="background:#66CCFF" cite="http://">1808</span></td><td><span style="background:#66CCFF" cite="http://">4294</span></td><td><span style="background:#c9c9c9" cite="http://">23760</span></td><td><span style="background:#c9c9c9" cite="http://">4165</span></td><td><span style="background:#c9c9c9" cite="http://">17140</span></td><td><span style="background:#CCFFFF" cite="http://">11759</span></td><td><span style="background:#CCFFFF" cite="http://">1426</span></td><td><span style="background:#CCFFFF" cite="http://">17941</span></td><td><span style="background:#CCFFFF" cite="http://">4742</span></td><td><span style="background:#CCFFFF" cite="http://">1385</span></td><td><span style="background:#CCFFFF" cite="http://">8043</span></td><td><span style="background:#FFFFCC" cite="http://">11148</span></td><td><span style="background:#FFFFCC" cite="http://">37595</span></td><td><span style="background:#FFFF66" cite="http://">7794</span></td><td><span style="background:#FFCC00" cite="http://">24077</span></td><td><span style="background:#FFCC00" cite="http://">3813</span></td><td><span style="background:#F4F4F4" cite="http://">648</span></td><td><span style="background:#F4F4F4" cite="http://">1607</span></td><td><span style="background:#F4F4F4" cite="http://">3746</span></td><td><span style="background:#F4F4F4" cite="http://">4146</span></td><td><span style="background:#FF99FF" cite="http://">6834</span></td><td><span style="background:#FF99FF" cite="http://">7372</span></td><td><span style="background:#FF99FF" cite="http://">5162</span></td><td><span style="background:#FF99FF" cite="http://">1072</span></td><td><span style="background:#FF99FF" cite="http://">1834</span></td><td><span style="background:#FF99FF" cite="http://">9876</span></td><td><span style="background:#f8f8f8" cite="http://">2607</span></td><td><span style="background:#f8f8f8" cite="http://">3902</span></td><td><span style="background:#f8f8f8" cite="http://">6838</span></td><td><span style="background:#CC99CC" cite="http://">6995</span></td><td><span style="background:#CC99CC" cite="http://">8161</span></td><td><span style="background:#CC99CC" cite="http://">2444</span></td><td><span style="background:#CC99CC" cite="http://">1195</span></td><td><span style="background:#99FFCC" cite="http://">3298</span></td><td><span style="background:#CCFF00" cite="http://">15345</span></td><td><span style="background:#CCFF00" cite="http://">4760</span></td><td><span style="background:#33FFCC" cite="http://">1204</span></td><td><span style="background:#33FFCC" cite="http://">2398</span></td><td><span style="background:#33FFCC" cite="http://">11350</span></td><td><span style="background:#33FFCC" cite="http://">6016</span></td></tr></table> | |||
<p><span style="background:#336699;color:white;padding:5px" cite="http://"><big><b>Relative Synonimous Codon Usage (RSCU)</b></big></span></p> | |||
<table><tr><td><span style="color:red" cite="http://"><span class="caps">CODON</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCC</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCA</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCG</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">AAC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">AAT</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">GAC</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">GAT</span></span></td><td><span style="background:#99CC99" cite="http://"><span class="caps">TGC</span></span></td><td><span style="background:#99CC99" cite="http://"><span class="caps">TGT</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">CAA</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">CAG</span></span></td><td><span style="background:#FF00CC" cite="http://"><span class="caps">GAG</span></span></td><td><span style="background:#FF00CC" cite="http://"><span class="caps">GAA</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGA</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGT</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGG</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGC</span></span></td><td><span style="background:#66CCFF" cite="http://"><span class="caps">CAC</span></span></td><td><span style="background:#66CCFF" cite="http://"><span class="caps">CAT</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATT</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATC</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTT</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTG</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">TTA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTC</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">TTG</span></span></td><td><span style="background:#FFFFCC" cite="http://"><span class="caps">AAG</span></span></td><td><span style="background:#FFFFCC" cite="http://"><span class="caps">AAA</span></span></td><td><span style="background:#FFFF66" cite="http://"><span class="caps">ATG</span></span></td><td><span style="background:#FFCC00" cite="http://"><span class="caps">TTT</span></span></td><td><span style="background:#FFCC00" cite="http://"><span class="caps">TTC</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCG</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCC</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCA</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGC</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCC</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCT</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TAG</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TGA</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TAA</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACT</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACA</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACG</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">TGG</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">TAT</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">TAC</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTC</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTG</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTT</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTA</span></span></td></tr><tr><td><span style="color:red" cite="http://"><span class="caps">AMINOACID</span></span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#CC99CC" cite="http://">Asn</span></td><td><span style="background:#CC99CC" cite="http://">Asn</span></td><td><span style="background:#99FFCC" cite="http://">Asp</span></td><td><span style="background:#99FFCC" cite="http://">Asp</span></td><td><span style="background:#99CC99" cite="http://">Cys</span></td><td><span style="background:#99CC99" cite="http://">Cys</span></td><td><span style="background:#CCFF00" cite="http://">Gln</span></td><td><span style="background:#CCFF00" cite="http://">Gln</span></td><td><span style="background:#FF00CC" cite="http://">Glu</span></td><td><span style="background:#FF00CC" cite="http://">Glu</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#66CCFF" cite="http://">His</span></td><td><span style="background:#66CCFF" cite="http://">His</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#FFFFCC" cite="http://">Lys</span></td><td><span style="background:#FFFFCC" cite="http://">Lys</span></td><td><span style="background:#FFFF66" cite="http://">Met</span></td><td><span style="background:#FFCC00" cite="http://">Phe</span></td><td><span style="background:#FFCC00" cite="http://">Phe</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#99FFCC" cite="http://">Trp</span></td><td><span style="background:#CCFF00" cite="http://">Tyr</span></td><td><span style="background:#CCFF00" cite="http://">Tyr</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td></tr><tr><td><span style="color:red" cite="http://"><span class="caps">RSCU</span></span></td><td><span style="background:#f4f4f4" cite="http://">0.44</span></td><td><span style="background:#f4f4f4" cite="http://">1.54</span></td><td><span style="background:#f4f4f4" cite="http://">0.26</span></td><td><span style="background:#f4f4f4" cite="http://">1.77</span></td><td><span style="background:#FF99FF" cite="http://">0.42</span></td><td><span style="background:#FF99FF" cite="http://">1.13</span></td><td><span style="background:#FF99FF" cite="http://">0.30</span></td><td><span style="background:#FF99FF" cite="http://">0.17</span></td><td><span style="background:#FF99FF" cite="http://">3.78</span></td><td><span style="background:#FF99FF" cite="http://">0.19</span></td><td><span style="background:#CC99CC" cite="http://">0.43</span></td><td><span style="background:#CC99CC" cite="http://">1.57</span></td><td><span style="background:#99FFCC" cite="http://">0.39</span></td><td><span style="background:#99FFCC" cite="http://">1.61</span></td><td><span style="background:#99CC99" cite="http://">0.84</span></td><td><span style="background:#99CC99" cite="http://">1.16</span></td><td><span style="background:#CCFF00" cite="http://">1.63</span></td><td><span style="background:#CCFF00" cite="http://">0.37</span></td><td><span style="background:#FF00CC" cite="http://">0.52</span></td><td><span style="background:#FF00CC" cite="http://">1.48</span></td><td><span style="background:#33FFCC" cite="http://">1.65</span></td><td><span style="background:#33FFCC" cite="http://">1.02</span></td><td><span style="background:#33FFCC" cite="http://">0.68</span></td><td><span style="background:#33FFCC" cite="http://">0.65</span></td><td><span style="background:#66CCFF" cite="http://">0.59</span></td><td><span style="background:#66CCFF" cite="http://">1.41</span></td><td><span style="background:#c9c9c9" cite="http://">1.58</span></td><td><span style="background:#c9c9c9" cite="http://">0.28</span></td><td><span style="background:#c9c9c9" cite="http://">1.14</span></td><td><span style="background:#CCFFFF" cite="http://">1.56</span></td><td><span style="background:#CCFFFF" cite="http://">0.19</span></td><td><span style="background:#CCFFFF" cite="http://">2.38</span></td><td><span style="background:#CCFFFF" cite="http://">0.63</span></td><td><span style="background:#CCFFFF" cite="http://">0.18</span></td><td><span style="background:#CCFFFF" cite="http://">1.07</span></td><td><span style="background:#FFFFCC" cite="http://">0.46</span></td><td><span style="background:#FFFFCC" cite="http://">1.54</span></td><td><span style="background:#FFFF66" cite="http://">1.00</span></td><td><span style="background:#FFCC00" cite="http://">1.73</span></td><td><span style="background:#FFCC00" cite="http://">0.27</span></td><td><span style="background:#F4F4F4" cite="http://">0.26</span></td><td><span style="background:#F4F4F4" cite="http://">0.63</span></td><td><span style="background:#F4F4F4" cite="http://">1.48</span></td><td><span style="background:#F4F4F4" cite="http://">1.63</span></td><td><span style="background:#FF99FF" cite="http://">1.28</span></td><td><span style="background:#FF99FF" cite="http://">1.38</span></td><td><span style="background:#FF99FF" cite="http://">0.96</span></td><td><span style="background:#FF99FF" cite="http://">0.20</span></td><td><span style="background:#FF99FF" cite="http://">0.34</span></td><td><span style="background:#FF99FF" cite="http://">1.84</span></td><td><span style="background:#f8f8f8" cite="http://">0.59</span></td><td><span style="background:#f8f8f8" cite="http://">0.88</span></td><td><span style="background:#f8f8f8" cite="http://">1.54</span></td><td><span style="background:#CC99CC" cite="http://">1.49</span></td><td><span style="background:#CC99CC" cite="http://">1.74</span></td><td><span style="background:#CC99CC" cite="http://">0.52</span></td><td><span style="background:#CC99CC" cite="http://">0.25</span></td><td><span style="background:#99FFCC" cite="http://">1.00</span></td><td><span style="background:#CCFF00" cite="http://">1.53</span></td><td><span style="background:#CCFF00" cite="http://">0.47</span></td><td><span style="background:#33FFCC" cite="http://">0.23</span></td><td><span style="background:#33FFCC" cite="http://">0.46</span></td><td><span style="background:#33FFCC" cite="http://">2.17</span></td><td><span style="background:#33FFCC" cite="http://">1.15</span></td></tr></table> | |||
<p><span style="background:#336699;color:white;padding:5px" cite="http://"><big><b>Relative Adaptiveness of Codon</b></big></span></p> | |||
<table><tr><td><span style="color:red" cite="http://"><span class="caps">CODON</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCC</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCA</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCG</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">CGC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">AAC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">AAT</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">GAC</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">GAT</span></span></td><td><span style="background:#99CC99" cite="http://"><span class="caps">TGC</span></span></td><td><span style="background:#99CC99" cite="http://"><span class="caps">TGT</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">CAA</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">CAG</span></span></td><td><span style="background:#FF00CC" cite="http://"><span class="caps">GAG</span></span></td><td><span style="background:#FF00CC" cite="http://"><span class="caps">GAA</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGA</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGT</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGG</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GGC</span></span></td><td><span style="background:#66CCFF" cite="http://"><span class="caps">CAC</span></span></td><td><span style="background:#66CCFF" cite="http://"><span class="caps">CAT</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATT</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATC</span></span></td><td><span style="background:#c9c9c9" cite="http://"><span class="caps">ATA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTT</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTG</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">TTA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTA</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">CTC</span></span></td><td><span style="background:#CCFFFF" cite="http://"><span class="caps">TTG</span></span></td><td><span style="background:#FFFFCC" cite="http://"><span class="caps">AAG</span></span></td><td><span style="background:#FFFFCC" cite="http://"><span class="caps">AAA</span></span></td><td><span style="background:#FFFF66" cite="http://"><span class="caps">ATG</span></span></td><td><span style="background:#FFCC00" cite="http://"><span class="caps">TTT</span></span></td><td><span style="background:#FFCC00" cite="http://"><span class="caps">TTC</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCG</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCC</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCA</span></span></td><td><span style="background:#F4F4F4" cite="http://"><span class="caps">CCT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGT</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCA</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">AGC</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCG</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCC</span></span></td><td><span style="background:#FF99FF" cite="http://"><span class="caps">TCT</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TAG</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TGA</span></span></td><td><span style="background:#f8f8f8" cite="http://"><span class="caps">TAA</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACT</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACA</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACC</span></span></td><td><span style="background:#CC99CC" cite="http://"><span class="caps">ACG</span></span></td><td><span style="background:#99FFCC" cite="http://"><span class="caps">TGG</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">TAT</span></span></td><td><span style="background:#CCFF00" cite="http://"><span class="caps">TAC</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTC</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTG</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTT</span></span></td><td><span style="background:#33FFCC" cite="http://"><span class="caps">GTA</span></span></td></tr><tr><td><span style="color:red" cite="http://"><span class="caps">AMINOACID</span></span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#f4f4f4" cite="http://">Ala</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#FF99FF" cite="http://">Arg</span></td><td><span style="background:#CC99CC" cite="http://">Asn</span></td><td><span style="background:#CC99CC" cite="http://">Asn</span></td><td><span style="background:#99FFCC" cite="http://">Asp</span></td><td><span style="background:#99FFCC" cite="http://">Asp</span></td><td><span style="background:#99CC99" cite="http://">Cys</span></td><td><span style="background:#99CC99" cite="http://">Cys</span></td><td><span style="background:#CCFF00" cite="http://">Gln</span></td><td><span style="background:#CCFF00" cite="http://">Gln</span></td><td><span style="background:#FF00CC" cite="http://">Glu</span></td><td><span style="background:#FF00CC" cite="http://">Glu</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#33FFCC" cite="http://">Gly</span></td><td><span style="background:#66CCFF" cite="http://">His</span></td><td><span style="background:#66CCFF" cite="http://">His</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#c9c9c9" cite="http://">Ile</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#CCFFFF" cite="http://">Leu</span></td><td><span style="background:#FFFFCC" cite="http://">Lys</span></td><td><span style="background:#FFFFCC" cite="http://">Lys</span></td><td><span style="background:#FFFF66" cite="http://">Met</span></td><td><span style="background:#FFCC00" cite="http://">Phe</span></td><td><span style="background:#FFCC00" cite="http://">Phe</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#F4F4F4" cite="http://">Pro</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#FF99FF" cite="http://">Ser</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#f8f8f8" cite="http://">Stop</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#CC99CC" cite="http://">Thr</span></td><td><span style="background:#99FFCC" cite="http://">Trp</span></td><td><span style="background:#CCFF00" cite="http://">Tyr</span></td><td><span style="background:#CCFF00" cite="http://">Tyr</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td><td><span style="background:#33FFCC" cite="http://">Val</span></td></tr><tr><td><span style="color:red" cite="http://"><span class="caps">RAC</span></span></td><td><span style="background:#f4f4f4" cite="http://">0.25</span></td><td><span style="background:#f4f4f4" cite="http://">0.87</span></td><td><span style="background:#f4f4f4" cite="http://">0.15</span></td><td><span style="background:#f4f4f4" cite="http://">1.00</span></td><td><span style="background:#FF99FF" cite="http://">0.11</span></td><td><span style="background:#FF99FF" cite="http://">0.30</span></td><td><span style="background:#FF99FF" cite="http://">0.08</span></td><td><span style="background:#FF99FF" cite="http://">0.04</span></td><td><span style="background:#FF99FF" cite="http://">1.00</span></td><td><span style="background:#FF99FF" cite="http://">0.05</span></td><td><span style="background:#CC99CC" cite="http://">0.27</span></td><td><span style="background:#CC99CC" cite="http://">1.00</span></td><td><span style="background:#99FFCC" cite="http://">0.24</span></td><td><span style="background:#99FFCC" cite="http://">1.00</span></td><td><span style="background:#99CC99" cite="http://">0.72</span></td><td><span style="background:#99CC99" cite="http://">1.00</span></td><td><span style="background:#CCFF00" cite="http://">1.00</span></td><td><span style="background:#CCFF00" cite="http://">0.23</span></td><td><span style="background:#FF00CC" cite="http://">0.35</span></td><td><span style="background:#FF00CC" cite="http://">1.00</span></td><td><span style="background:#33FFCC" cite="http://">1.00</span></td><td><span style="background:#33FFCC" cite="http://">0.62</span></td><td><span style="background:#33FFCC" cite="http://">0.41</span></td><td><span style="background:#33FFCC" cite="http://">0.39</span></td><td><span style="background:#66CCFF" cite="http://">0.42</span></td><td><span style="background:#66CCFF" cite="http://">1.00</span></td><td><span style="background:#c9c9c9" cite="http://">1.00</span></td><td><span style="background:#c9c9c9" cite="http://">0.18</span></td><td><span style="background:#c9c9c9" cite="http://">0.72</span></td><td><span style="background:#CCFFFF" cite="http://">0.66</span></td><td><span style="background:#CCFFFF" cite="http://">0.08</span></td><td><span style="background:#CCFFFF" cite="http://">1.00</span></td><td><span style="background:#CCFFFF" cite="http://">0.26</span></td><td><span style="background:#CCFFFF" cite="http://">0.08</span></td><td><span style="background:#CCFFFF" cite="http://">0.45</span></td><td><span style="background:#FFFFCC" cite="http://">0.30</span></td><td><span style="background:#FFFFCC" cite="http://">1.00</span></td><td><span style="background:#FFFF66" cite="http://">1.00</span></td><td><span style="background:#FFCC00" cite="http://">1.00</span></td><td><span style="background:#FFCC00" cite="http://">0.16</span></td><td><span style="background:#F4F4F4" cite="http://">0.16</span></td><td><span style="background:#F4F4F4" cite="http://">0.39</span></td><td><span style="background:#F4F4F4" cite="http://">0.90</span></td><td><span style="background:#F4F4F4" cite="http://">1.00</span></td><td><span style="background:#FF99FF" cite="http://">0.69</span></td><td><span style="background:#FF99FF" cite="http://">0.75</span></td><td><span style="background:#FF99FF" cite="http://">0.52</span></td><td><span style="background:#FF99FF" cite="http://">0.11</span></td><td><span style="background:#FF99FF" cite="http://">0.19</span></td><td><span style="background:#FF99FF" cite="http://">1.00</span></td><td><span style="background:#f8f8f8" cite="http://">0.38</span></td><td><span style="background:#f8f8f8" cite="http://">0.57</span></td><td><span style="background:#f8f8f8" cite="http://">1.00</span></td><td><span style="background:#CC99CC" cite="http://">0.86</span></td><td><span style="background:#CC99CC" cite="http://">1.00</span></td><td><span style="background:#CC99CC" cite="http://">0.30</span></td><td><span style="background:#CC99CC" cite="http://">0.15</span></td><td><span style="background:#99FFCC" cite="http://">1.00</span></td><td><span style="background:#CCFF00" cite="http://">1.00</span></td><td><span style="background:#CCFF00" cite="http://">0.31</span></td><td><span style="background:#33FFCC" cite="http://">0.11</span></td><td><span style="background:#33FFCC" cite="http://">0.21</span></td><td><span style="background:#33FFCC" cite="http://">1.00</span></td><td><span style="background:#33FFCC" cite="http://">0.53</span></td></tr></table> | |||
<p><span style="background:#336699;color:white;padding:5px" cite="http://"><big><b>Monomers</b></big></span></p> | |||
<table><tr><td><span style="color:red" cite="http://">A</span></td><td>524241</td></tr><tr><td><span style="color:red" cite="http://">T</span></td><td>440303</td></tr><tr><td><span style="color:red" cite="http://">G</span></td><td>225741</td></tr><tr><td><span style="color:red" cite="http://">C</span></td><td>165502</td></tr></table> | |||
| Line 126: | Line 150: | ||
{| class="wikitable" | {| class="wikitable" | ||
| BBA15 || [[file:hist 1| | | BBA15 || [[file:hist 1.png| 600px]] | ||
|- | |- | ||
| BBA24 || [[file:hist 2| | | BBA24 || [[file:hist 2.png| 600px]] | ||
|- | |- | ||
| BBA68 || [[file:hist 3| | | BBA68 || [[file:hist 3.png| 600px]] | ||
|- | |- | ||
| BBB 18|| [[file:hist 1| | | BBB 18|| [[file:hist 1.png| 600px]] | ||
|- | |- | ||
| Whole genome || [[file:hist 5| | | Whole genome || [[file:hist 5.png| 600px]] | ||
|} | |} | ||
Latest revision as of 21:08, 31 July 2013
Data
Report for BBA15
Codon Adaptation Index (CAI) for sequence : 0.47
GC percentage for sequence : 33.58%
GENETIC CODE USED : 1 <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">more about genetic code</a>
CODON USAGE
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| COUNT | 1 | 5 | O | 7 | O | O | O | O | 2 | O | 6 | 7 | 11 | 7 | O | 1 | 4 | O | 4 | 19 | 10 | 4 | 2 | 6 | O | O | 8 | O | 5 | 11 | O | 9 | 5 | O | 3 | 4 | 39 | 2 | 1 | 2 | O | O | O | 1 | 4 | 10 | 6 | O | 1 | 6 | O | O | O | 13 | 14 | 3 | O | 1 | 2 | 3 | O | 2 | 11 | 11 |
Relative Synonimous Codon Usage (RSCU)
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RSCU | 0.31 | 1.54 | 0.00 | 2.15 | 0.00 | 0.00 | 0.00 | 0.00 | 6.00 | 0.00 | 0.92 | 1.08 | 1.22 | 0.78 | 0.00 | 2.00 | 2.00 | 0.00 | 0.35 | 1.65 | 1.82 | 0.73 | 0.36 | 1.09 | 0.00 | 0.00 | 1.85 | 0.00 | 1.15 | 2.36 | 0.00 | 1.93 | 1.07 | 0.00 | 0.64 | 0.19 | 1.81 | 1.00 | 0.67 | 1.33 | 0.00 | 0.00 | 0.00 | 4.00 | 0.89 | 2.22 | 1.33 | 0.00 | 0.22 | 1.33 | 0.00 | 0.00 | 0.00 | 1.73 | 1.87 | 0.40 | 0.00 | 1.00 | 0.80 | 1.20 | 0.00 | 0.33 | 1.83 | 1.83 |
Relative Adaptiveness of Codon
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RAC | 0.14 | 0.71 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.86 | 1.00 | 1.00 | 0.64 | 0.00 | 1.00 | 1.00 | 0.00 | 0.21 | 1.00 | 1.00 | 0.40 | 0.20 | 0.60 | 0.00 | 0.00 | 1.00 | 0.00 | 0.62 | 1.00 | 0.00 | 0.82 | 0.45 | 0.00 | 0.27 | 0.10 | 1.00 | 1.00 | 0.50 | 1.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.40 | 1.00 | 0.60 | 0.00 | 0.10 | 0.60 | 0.00 | 0.00 | 0.00 | 0.93 | 1.00 | 0.21 | 0.00 | 1.00 | 0.67 | 1.00 | 0.00 | 0.18 | 1.00 | 1.00 |
Monomers
| A | 352 |
| T | 192 |
| G | 154 |
| C | 121 |
<a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.
Report for BBA24
Codon Adaptation Index (CAI) for sequence : 0.50
GC percentage for sequence : 32.46%
GENETIC CODE USED : 1 <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">more about genetic code</a>
CODON USAGE
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| COUNT | 1 | 7 | 1 | 7 | 2 | 1 | O | O | 2 | O | 4 | 8 | 2 | 7 | 2 | 2 | 4 | O | 3 | 15 | 5 | 2 | 1 | 1 | O | 1 | 5 | O | 7 | 7 | O | 5 | 3 | 1 | 1 | 3 | 24 | 5 | 6 | 2 | O | O | 3 | 1 | 3 | 5 | 1 | O | O | 1 | O | O | O | 8 | 8 | 1 | 1 | O | 1 | 1 | 2 | 2 | 2 | 4 |
Relative Synonimous Codon Usage (RSCU)
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RSCU | 0.25 | 1.75 | 0.25 | 1.75 | 2.40 | 1.20 | 0.00 | 0.00 | 2.40 | 0.00 | 0.67 | 1.33 | 0.44 | 1.56 | 1.00 | 1.00 | 2.00 | 0.00 | 0.33 | 1.67 | 2.22 | 0.89 | 0.44 | 0.44 | 0.00 | 2.00 | 1.25 | 0.00 | 1.75 | 2.47 | 0.00 | 1.76 | 1.06 | 0.35 | 0.35 | 0.22 | 1.78 | 1.00 | 1.50 | 0.50 | 0.00 | 0.00 | 3.00 | 1.00 | 1.80 | 3.00 | 0.60 | 0.00 | 0.00 | 0.60 | 0.00 | 0.00 | 0.00 | 1.78 | 1.78 | 0.22 | 0.22 | 0.00 | 1.00 | 1.00 | 0.80 | 0.80 | 0.80 | 1.60 |
Relative Adaptiveness of Codon
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RAC | 0.14 | 1.00 | 0.14 | 1.00 | 1.00 | 0.50 | 0.00 | 0.00 | 1.00 | 0.00 | 0.50 | 1.00 | 0.29 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.20 | 1.00 | 1.00 | 0.40 | 0.20 | 0.20 | 0.00 | 1.00 | 0.71 | 0.00 | 1.00 | 1.00 | 0.00 | 0.71 | 0.43 | 0.14 | 0.14 | 0.13 | 1.00 | 1.00 | 1.00 | 0.33 | 0.00 | 0.00 | 1.00 | 0.33 | 0.60 | 1.00 | 0.20 | 0.00 | 0.00 | 0.20 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.13 | 0.13 | 0.00 | 1.00 | 1.00 | 0.50 | 0.50 | 0.50 | 1.00 |
Monomers
| A | 248 |
| T | 139 |
| G | 102 |
| C | 84 |
<a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.
Report for BBA68
Codon Adaptation Index (CAI) for sequence : 0.48
GC percentage for sequence : 27.62%
GENETIC CODE USED : 1 <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">more about genetic code</a>
CODON USAGE
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| COUNT | 2 | 6 | O | 3 | O | O | O | O | 3 | O | 4 | 16 | 1 | 12 | 2 | O | 13 | O | 4 | 21 | 3 | 2 | 1 | 1 | 2 | 1 | 12 | 5 | 14 | 7 | 2 | 9 | 5 | O | 3 | 4 | 33 | 4 | 7 | 2 | 1 | O | 1 | 4 | 1 | 5 | 3 | O | 2 | 4 | O | O | O | 8 | O | 4 | 1 | 1 | 3 | 6 | O | O | 2 | 1 |
Relative Synonimous Codon Usage (RSCU)
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RSCU | 0.73 | 2.18 | 0.00 | 1.09 | 0.00 | 0.00 | 0.00 | 0.00 | 6.00 | 0.00 | 0.40 | 1.60 | 0.15 | 1.85 | 2.00 | 0.00 | 2.00 | 0.00 | 0.32 | 1.68 | 1.71 | 1.14 | 0.57 | 0.57 | 1.33 | 0.67 | 1.16 | 0.48 | 1.35 | 1.62 | 0.46 | 2.08 | 1.15 | 0.00 | 0.69 | 0.22 | 1.78 | 1.00 | 1.56 | 0.44 | 0.67 | 0.00 | 0.67 | 2.67 | 0.40 | 2.00 | 1.20 | 0.00 | 0.80 | 1.60 | 0.00 | 0.00 | 0.00 | 2.46 | 0.00 | 1.23 | 0.31 | 1.00 | 0.67 | 1.33 | 0.00 | 0.00 | 2.67 | 1.33 |
Relative Adaptiveness of Codon
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RAC | 0.33 | 1.00 | 0.00 | 0.50 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.25 | 1.00 | 0.08 | 1.00 | 1.00 | 0.00 | 1.00 | 0.00 | 0.19 | 1.00 | 1.00 | 0.67 | 0.33 | 0.33 | 1.00 | 0.50 | 0.86 | 0.36 | 1.00 | 0.78 | 0.22 | 1.00 | 0.56 | 0.00 | 0.33 | 0.12 | 1.00 | 1.00 | 1.00 | 0.29 | 0.25 | 0.00 | 0.25 | 1.00 | 0.20 | 1.00 | 0.60 | 0.00 | 0.40 | 0.80 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.50 | 0.13 | 1.00 | 0.50 | 1.00 | 0.00 | 0.00 | 1.00 | 0.50 |
Monomers
| A | 346 |
| T | 199 |
| G | 97 |
| C | 111 |
<a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.
Report for BBB18
Codon Adaptation Index (CAI) for sequence : 0.50
GC percentage for sequence : 29.17%
GENETIC CODE USED : 1 <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">more about genetic code</a>
CODON USAGE
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| COUNT | 1 | 6 | O | 9 | O | 2 | 1 | 1 | 11 | 1 | 5 | 24 | 7 | 15 | 3 | 4 | 21 | 1 | 3 | 36 | 15 | 5 | 3 | 7 | 1 | 6 | 29 | 7 | 30 | 10 | O | 20 | 11 | 2 | 10 | 10 | 42 | 9 | 19 | 4 | O | 1 | 6 | 11 | 7 | 9 | 4 | O | 1 | 20 | O | O | O | 10 | 9 | 4 | O | 3 | 17 | 5 | 1 | 2 | 13 | 14 |
Relative Synonimous Codon Usage (RSCU)
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RSCU | 0.25 | 1.50 | 0.00 | 2.25 | 0.00 | 0.75 | 0.38 | 0.38 | 4.13 | 0.38 | 0.34 | 1.66 | 0.64 | 1.36 | 0.86 | 1.14 | 1.91 | 0.09 | 0.15 | 1.85 | 2.00 | 0.67 | 0.40 | 0.93 | 0.29 | 1.71 | 1.32 | 0.32 | 1.36 | 1.13 | 0.00 | 2.26 | 1.25 | 0.23 | 1.13 | 0.38 | 1.62 | 1.00 | 1.65 | 0.35 | 0.00 | 0.22 | 1.33 | 2.44 | 1.02 | 1.32 | 0.59 | 0.00 | 0.15 | 2.93 | 0.00 | 0.00 | 0.00 | 1.74 | 1.57 | 0.70 | 0.00 | 1.00 | 1.55 | 0.45 | 0.13 | 0.27 | 1.73 | 1.87 |
Relative Adaptiveness of Codon
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RAC | 0.11 | 0.67 | 0.00 | 1.00 | 0.00 | 0.18 | 0.09 | 0.09 | 1.00 | 0.09 | 0.21 | 1.00 | 0.47 | 1.00 | 0.75 | 1.00 | 1.00 | 0.05 | 0.08 | 1.00 | 1.00 | 0.33 | 0.20 | 0.47 | 0.17 | 1.00 | 0.97 | 0.23 | 1.00 | 0.50 | 0.00 | 1.00 | 0.55 | 0.10 | 0.50 | 0.24 | 1.00 | 1.00 | 1.00 | 0.21 | 0.00 | 0.09 | 0.55 | 1.00 | 0.35 | 0.45 | 0.20 | 0.00 | 0.05 | 1.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.90 | 0.40 | 0.00 | 1.00 | 1.00 | 0.29 | 0.07 | 0.14 | 0.93 | 1.00 |
Monomers
| A | 626 |
| T | 496 |
| G | 248 |
| C | 214 |
<a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.
Report for Whole Genome
Codon Adaptation Index (CAI) for sequence : 0.57
GC percentage for sequence : 28.86%
GENETIC CODE USED : 1 <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">more about genetic code</a>
CODON USAGE
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| COUNT | 2000 | 7080 | 1187 | 8110 | 1277 | 3427 | 913 | 512 | 11465 | 584 | 6857 | 25195 | 3762 | 15623 | 2397 | 3330 | 9874 | 2224 | 6834 | 19297 | 8360 | 5151 | 3452 | 3285 | 1808 | 4294 | 23760 | 4165 | 17140 | 11759 | 1426 | 17941 | 4742 | 1385 | 8043 | 11148 | 37595 | 7794 | 24077 | 3813 | 648 | 1607 | 3746 | 4146 | 6834 | 7372 | 5162 | 1072 | 1834 | 9876 | 2607 | 3902 | 6838 | 6995 | 8161 | 2444 | 1195 | 3298 | 15345 | 4760 | 1204 | 2398 | 11350 | 6016 |
Relative Synonimous Codon Usage (RSCU)
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RSCU | 0.44 | 1.54 | 0.26 | 1.77 | 0.42 | 1.13 | 0.30 | 0.17 | 3.78 | 0.19 | 0.43 | 1.57 | 0.39 | 1.61 | 0.84 | 1.16 | 1.63 | 0.37 | 0.52 | 1.48 | 1.65 | 1.02 | 0.68 | 0.65 | 0.59 | 1.41 | 1.58 | 0.28 | 1.14 | 1.56 | 0.19 | 2.38 | 0.63 | 0.18 | 1.07 | 0.46 | 1.54 | 1.00 | 1.73 | 0.27 | 0.26 | 0.63 | 1.48 | 1.63 | 1.28 | 1.38 | 0.96 | 0.20 | 0.34 | 1.84 | 0.59 | 0.88 | 1.54 | 1.49 | 1.74 | 0.52 | 0.25 | 1.00 | 1.53 | 0.47 | 0.23 | 0.46 | 2.17 | 1.15 |
Relative Adaptiveness of Codon
| CODON | GCC | GCA | GCG | GCT | CGA | AGG | CGT | CGG | AGA | CGC | AAC | AAT | GAC | GAT | TGC | TGT | CAA | CAG | GAG | GAA | GGA | GGT | GGG | GGC | CAC | CAT | ATT | ATC | ATA | CTT | CTG | TTA | CTA | CTC | TTG | AAG | AAA | ATG | TTT | TTC | CCG | CCC | CCA | CCT | AGT | TCA | AGC | TCG | TCC | TCT | TAG | TGA | TAA | ACT | ACA | ACC | ACG | TGG | TAT | TAC | GTC | GTG | GTT | GTA |
| AMINOACID | Ala | Ala | Ala | Ala | Arg | Arg | Arg | Arg | Arg | Arg | Asn | Asn | Asp | Asp | Cys | Cys | Gln | Gln | Glu | Glu | Gly | Gly | Gly | Gly | His | His | Ile | Ile | Ile | Leu | Leu | Leu | Leu | Leu | Leu | Lys | Lys | Met | Phe | Phe | Pro | Pro | Pro | Pro | Ser | Ser | Ser | Ser | Ser | Ser | Stop | Stop | Stop | Thr | Thr | Thr | Thr | Trp | Tyr | Tyr | Val | Val | Val | Val |
| RAC | 0.25 | 0.87 | 0.15 | 1.00 | 0.11 | 0.30 | 0.08 | 0.04 | 1.00 | 0.05 | 0.27 | 1.00 | 0.24 | 1.00 | 0.72 | 1.00 | 1.00 | 0.23 | 0.35 | 1.00 | 1.00 | 0.62 | 0.41 | 0.39 | 0.42 | 1.00 | 1.00 | 0.18 | 0.72 | 0.66 | 0.08 | 1.00 | 0.26 | 0.08 | 0.45 | 0.30 | 1.00 | 1.00 | 1.00 | 0.16 | 0.16 | 0.39 | 0.90 | 1.00 | 0.69 | 0.75 | 0.52 | 0.11 | 0.19 | 1.00 | 0.38 | 0.57 | 1.00 | 0.86 | 1.00 | 0.30 | 0.15 | 1.00 | 1.00 | 0.31 | 0.11 | 0.21 | 1.00 | 0.53 |
Monomers
| A | 524241 |
| T | 440303 |
| G | 225741 |
| C | 165502 |
<a href="http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-1.05/lib/Bio/Tools/CodonOptTable.pm">Source code</a> is available.
Charts
| BBA15 | 
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| BBA24 | 
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| BBA68 | 
|
| BBB 18 |
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| Whole genome | 
|
Hypothesis & Background
- Central Hypothesis: Borrelia host-interacting genes show optimal codon usage
- Background/Rationale:
- Borrelia is an obligate, non-free-living parasite of vertebrates. A large number of genes are devoted to host invasion and to surviving the host immune defense.
- Evolutionary theory predicts that highly expressed genes use the most abundant tRNA in the cell, and, as a result, they tend to show strong codon usage biases
- We expect Borrelia host-interacting, virulence-conferring genes use more optimal codons than housekeeping genes
- Importance: If the hypothesis is supported, it would establish a new computational method to identify host-interacting virulence genes based on genome analysis.
Data & Overview
- Data Set: The Borrelia burgdorferi B31 genome sequences, N=1500 genes
- Identify host-interacting genes and a set of housekeeping genes
- Calculate the Codon Usage Adaptation Index for each gene
- Test if the biases are significantly different between the virulence genes vs the house keeping genes
- Presentation, Report, & Future directions
Essential Computing skills
- Operating System: Linux/Ubuntu
- Programming Languages: BASH, Perl/BioPerl
- Database Language: SQL
- Statistical Language: R
Essential Readings
- Note: I will post some of the PDFs later
- Borrelia burgdorferi & Lyme disease: A Review
- Codon Usage Biases: Wikipedia
- Borrelia gene regulation: A Review
- Identification of Borrelia virulence genes: A genome-wide expression study
Weigang 11:38, 10 May 2013 (EDT)