https://wiki.yeastgenome.org/index.php?action=history&feed=atom&title=S._cerevisiae_Codon_Usage_Tables 2026-08-20T04:24:45Z Revision history for this page on the wiki MediaWiki 1.31.14 https://wiki.yeastgenome.org/index.php?title=S._cerevisiae_Codon_Usage_Tables&diff=398954&oldid=prev 2014-09-29T16:34:07Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:34, 29 September 2014</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>==<del class="diffchange diffchange-inline">These tables are from 1999 and were built </del>using <del class="diffchange diffchange-inline">the known or predicted ORF sequences contained within the complete yeast genomic sequence.</del>==</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== <ins class="diffchange diffchange-inline">January 2011 Codon Usage (genome version 64-1-1) produced </ins>using <ins class="diffchange diffchange-inline">EMBOSS cusp</ins>==</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://<del class="diffchange diffchange-inline">downloads</del>.<del class="diffchange diffchange-inline">yeastgenome</del>.<del class="diffchange diffchange-inline">org</del>/unpublished_data/codon/<del class="diffchange diffchange-inline">ysc</del>.<del class="diffchange diffchange-inline">gene</del>.<del class="diffchange diffchange-inline">cod ''Saccharomyces cerevisiae''</del>] <del class="diffchange diffchange-inline">from 3</del>,<del class="diffchange diffchange-inline">222 </del>ORFs <del class="diffchange diffchange-inline">which have been assigned a gene name by the community as listed within SGD as of January 1999</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://<ins class="diffchange diffchange-inline">bun-dev</ins>.<ins class="diffchange diffchange-inline">stanford</ins>.<ins class="diffchange diffchange-inline">edu</ins>/unpublished_data/codon/<ins class="diffchange diffchange-inline">64_1_1_all_nuclear</ins>.<ins class="diffchange diffchange-inline">cusp 64_1_1_all_nuclear</ins>.<ins class="diffchange diffchange-inline">cusp</ins>] <ins class="diffchange diffchange-inline">for all ORFs (5865) encoded in the nuclear genome except the dubious ORFs and pseudogenes (i.e. including all verified</ins>, <ins class="diffchange diffchange-inline">uncharacterized </ins>ORFs <ins class="diffchange diffchange-inline">and transposable element genes without stop codons in them)</ins>.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://<del class="diffchange diffchange-inline">downloads</del>.<del class="diffchange diffchange-inline">yeastgenome</del>.<del class="diffchange diffchange-inline">org</del>/unpublished_data/codon/<del class="diffchange diffchange-inline">ysc</del>.<del class="diffchange diffchange-inline">orf</del>.<del class="diffchange diffchange-inline">cod ''Saccharomyces cerevisiae''</del>] <del class="diffchange diffchange-inline">from 6,222 </del>ORFs <del class="diffchange diffchange-inline">listed within SGD as of January 1999</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://<ins class="diffchange diffchange-inline">bun-dev</ins>.<ins class="diffchange diffchange-inline">stanford</ins>.<ins class="diffchange diffchange-inline">edu</ins>/unpublished_data/codon/<ins class="diffchange diffchange-inline">64_1_1_dubious</ins>.<ins class="diffchange diffchange-inline">cusp 64_1_1_dubious</ins>.<ins class="diffchange diffchange-inline">cusp</ins>] <ins class="diffchange diffchange-inline">for all nuclearly encoded dubious </ins>ORFs <ins class="diffchange diffchange-inline">(801)</ins>.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&lt;br&gt;</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">*[http://bun-dev.stanford.edu/unpublished_data/codon/64_1_1_mito.cusp 64_1_1_mito.cusp] for all mitochondrial non-dubious ORFs (19).</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>==<del class="diffchange diffchange-inline">These tables are </del>from 1993 <del class="diffchange diffchange-inline">and </del>produced <del class="diffchange diffchange-inline">with the </del>GCG <del class="diffchange diffchange-inline">program </del>CodonFrequency<del class="diffchange diffchange-inline">.</del>==</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== <ins class="diffchange diffchange-inline">June 2008 Codon Usage (genome version 61-1-1) produced using GCG CodonFrequency==</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">All known or predicted ORF sequences contained within the complete yeast genomic sequence were included.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">* [http://downloads.yeastgenome.org/unpublished_data/codon/s_cerevisiae-codonusage.txt s_cerevisiae-codonusage.txt]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">==January 1999 Codon Usage (genome version 12-1-1) produced using GCG CodonFrequency==</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">All known or predicted ORF sequences contained within the complete yeast genomic sequence were included.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">*[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.gene.cod ysc.gene.cod] from 3,222 ORFs assigned a gene name by the community as listed within SGD.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">*[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.orf.cod ysc.orf.cod] from 6,222 ORFs listed within SGD.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">*[http://downloads.yeastgenome.org/unpublished_data/codon/yscmt.cod yscmt.cod] </ins>from <ins class="diffchange diffchange-inline">28 mitochondrion genes in [http://www.yeastgenome.org/reference/S000058438/overview Foury F, et al. (1998)]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">==</ins>1993 <ins class="diffchange diffchange-inline">Codon Usage </ins>produced <ins class="diffchange diffchange-inline">using </ins>GCG CodonFrequency==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Duplicates, pseudogenes, mutant and synthetic genes were not included. Coding regions were specified using the Feature Table of each entry, then checked for accuracy. If more than one stop codon was found the sequence was not included.</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Duplicates, pseudogenes, mutant and synthetic genes were not included. Coding regions were specified using the Feature Table of each entry, then checked for accuracy. If more than one stop codon was found the sequence was not included.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.g63.cod <del class="diffchange diffchange-inline">''Saccharomyces cerevisiae''] from 435 genes found in GenBank 63.</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.g63.cod <ins class="diffchange diffchange-inline">ysc</ins>.<ins class="diffchange diffchange-inline">g63</ins>.cod] <ins class="diffchange diffchange-inline">from 435 </ins>genes found in GenBank 63 <ins class="diffchange diffchange-inline">(March 1990)</ins>.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">*[http://downloads.yeastgenome</del>.<del class="diffchange diffchange-inline">org/unpublished_data/codon/yscmt</del>.cod <del class="diffchange diffchange-inline">''Saccharomyces cerevisiae'' mitochondrion</del>] <del class="diffchange diffchange-inline">17 </del>genes found in GenBank 63.</div></td><td colspan="2">&#160;</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*[http://www.kazusa.or.jp/codon/ Codon Usage Database] from Yasukazu Nakamura using the latest GenBank Release.</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*[http://www.kazusa.or.jp/codon/ Codon Usage Database] from Yasukazu Nakamura using the latest GenBank Release.</div></td></tr> </table>

Gail https://wiki.yeastgenome.org/index.php?title=S._cerevisiae_Codon_Usage_Tables&diff=398822&oldid=prev 2014-04-09T15:35:40Z

<p>Created page with &quot;==These tables are from 1999 and were built using the known or predicted ORF sequences contained within the complete yeast genomic sequence.== *[http://downloads.yeastgenome.o...&quot;</p> <p><b>New page</b></p><div>==These tables are from 1999 and were built using the known or predicted ORF sequences contained within the complete yeast genomic sequence.==<br /> *[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.gene.cod ''Saccharomyces cerevisiae''] from 3,222 ORFs which have been assigned a gene name by the community as listed within SGD as of January 1999.<br /> *[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.orf.cod ''Saccharomyces cerevisiae''] from 6,222 ORFs listed within SGD as of January 1999.<br /> &lt;br&gt;<br /> <br /> ==These tables are from 1993 and produced with the GCG program CodonFrequency.==<br /> Duplicates, pseudogenes, mutant and synthetic genes were not included. Coding regions were specified using the Feature Table of each entry, then checked for accuracy. If more than one stop codon was found the sequence was not included.<br /> *[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.g63.cod ''Saccharomyces cerevisiae''] from 435 genes found in GenBank 63.<br /> *[http://downloads.yeastgenome.org/unpublished_data/codon/yscmt.cod ''Saccharomyces cerevisiae'' mitochondrion] 17 genes found in GenBank 63.<br /> *[http://www.kazusa.or.jp/codon/ Codon Usage Database] from Yasukazu Nakamura using the latest GenBank Release.</div>

Kyla