https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Mpetredi_Week_4 Mpetredi Week 4 - Revision history 2026-04-04T07:47:50Z Revision history for this page on the wiki MediaWiki 1.20.3 https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Mpetredi_Week_4&diff=1955&oldid=prev Mpetredi: added sig 2013-09-20T05:39:44Z <p>added sig</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:39, 20 September 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 31:</td> <td colspan="2" class="diff-lineno">Line 31:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*All commands in one string</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*All commands in one string</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>cat infA-E.coli-K12.txt | sed &quot;s/cat[at]at/ &lt;minus10box&gt;&amp;&lt;\/minus10box&gt; /g&quot; | sed -r &quot;s/.{17} &lt;minus10box&gt;/ &lt;\/minus35box&gt; &amp;/g&quot; | sed &quot;s/tt[gt]ac[at] &lt;\/minus35box&gt;/ &lt;minus35box&gt; &amp;/g&quot;&#160; | sed &quot;s/gagg/ &lt;rbs&gt;&amp;&lt;\/rbs&gt; /g&quot; | sed &quot;s/&lt;\/rbs&gt;/&amp;\n/g&quot; | sed &quot;2s/atg/ &lt;start_codon&gt;&amp;&lt;\/start_codon&gt; /1&quot; | sed &quot;s/.../ \n /3&quot; | sed &quot;s/aaaaggt...........gcctttt..../ &lt;terminator&gt;&amp;&lt;\/terminator&gt; /g&quot; | sed &quot;2s/atg/&lt;tss&gt;&amp;&lt;\/tss&gt; /1&quot; | sed &quot;s/tag/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot; | sed &quot;s/tga/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot; | sed &quot;s/taa/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>cat infA-E.coli-K12.txt | sed &quot;s/cat[at]at/ &lt;minus10box&gt;&amp;&lt;\/minus10box&gt; /g&quot; | sed -r &quot;s/.{17} &lt;minus10box&gt;/ &lt;\/minus35box&gt; &amp;/g&quot; | sed &quot;s/tt[gt]ac[at] &lt;\/minus35box&gt;/ &lt;minus35box&gt; &amp;/g&quot;&#160; | sed &quot;s/gagg/ &lt;rbs&gt;&amp;&lt;\/rbs&gt; /g&quot; | sed &quot;s/&lt;\/rbs&gt;/&amp;\n/g&quot; | sed &quot;2s/atg/ &lt;start_codon&gt;&amp;&lt;\/start_codon&gt; /1&quot; | sed &quot;s/.../ \n /3&quot; | sed &quot;s/aaaaggt...........gcctttt..../ &lt;terminator&gt;&amp;&lt;\/terminator&gt; /g&quot; | sed &quot;2s/atg/&lt;tss&gt;&amp;&lt;\/tss&gt; /1&quot; | sed &quot;s/tag/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot; | sed &quot;s/tga/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot; | sed &quot;s/taa/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[User:Mpetredi|Mpetredi]] ([[User talk:Mpetredi|talk]]) 22:39, 19 September 2013 (PDT)Mitchell Petredis</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category: Individual Homework]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category: Individual Homework]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category: Journal Entry]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category: Journal Entry]]</div></td></tr> </table> Mpetredi https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Mpetredi_Week_4&diff=1936&oldid=prev Mpetredi: added link to my user page 2013-09-20T05:18:32Z <p>added link to my user page</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:18, 20 September 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">{{mpetredi}}</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* -35 box of the promoter &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* -35 box of the promoter &#160;</div></td></tr> </table> Mpetredi https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Mpetredi_Week_4&diff=1933&oldid=prev Mpetredi: added categories 2013-09-20T05:17:15Z <p>added categories</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:17, 20 September 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 29:</td> <td colspan="2" class="diff-lineno">Line 29:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*All commands in one string</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*All commands in one string</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>cat infA-E.coli-K12.txt | sed &quot;s/cat[at]at/ &lt;minus10box&gt;&amp;&lt;\/minus10box&gt; /g&quot; | sed -r &quot;s/.{17} &lt;minus10box&gt;/ &lt;\/minus35box&gt; &amp;/g&quot; | sed &quot;s/tt[gt]ac[at] &lt;\/minus35box&gt;/ &lt;minus35box&gt; &amp;/g&quot;&#160; | sed &quot;s/gagg/ &lt;rbs&gt;&amp;&lt;\/rbs&gt; /g&quot; | sed &quot;s/&lt;\/rbs&gt;/&amp;\n/g&quot; | sed &quot;2s/atg/ &lt;start_codon&gt;&amp;&lt;\/start_codon&gt; /1&quot; | sed &quot;s/.../ \n /3&quot; | sed &quot;s/aaaaggt...........gcctttt..../ &lt;terminator&gt;&amp;&lt;\/terminator&gt; /g&quot; | sed &quot;2s/atg/&lt;tss&gt;&amp;&lt;\/tss&gt; /1&quot; | sed &quot;s/tag/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot; | sed &quot;s/tga/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot; | sed &quot;s/taa/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>cat infA-E.coli-K12.txt | sed &quot;s/cat[at]at/ &lt;minus10box&gt;&amp;&lt;\/minus10box&gt; /g&quot; | sed -r &quot;s/.{17} &lt;minus10box&gt;/ &lt;\/minus35box&gt; &amp;/g&quot; | sed &quot;s/tt[gt]ac[at] &lt;\/minus35box&gt;/ &lt;minus35box&gt; &amp;/g&quot;&#160; | sed &quot;s/gagg/ &lt;rbs&gt;&amp;&lt;\/rbs&gt; /g&quot; | sed &quot;s/&lt;\/rbs&gt;/&amp;\n/g&quot; | sed &quot;2s/atg/ &lt;start_codon&gt;&amp;&lt;\/start_codon&gt; /1&quot; | sed &quot;s/.../ \n /3&quot; | sed &quot;s/aaaaggt...........gcctttt..../ &lt;terminator&gt;&amp;&lt;\/terminator&gt; /g&quot; | sed &quot;2s/atg/&lt;tss&gt;&amp;&lt;\/tss&gt; /1&quot; | sed &quot;s/tag/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot; | sed &quot;s/tga/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot; | sed &quot;s/taa/ &lt;stop_codon&gt;&amp;&lt;\/stop_codon&gt; /3&quot;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Category: Individual Homework]]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Category: Journal Entry]]</ins></div></td></tr> </table> Mpetredi  
#**cat infA-E.coli-K12.txt | sed "s/aaaaggt...........gcctttt..../ <terminator>&<\/terminator> /g"
 
#**cat infA-E.coli-K12.txt | sed "s/aaaaggt...........gcctttt..../ <terminator>&<\/terminator> /g"
 
# What is the ''exact'' mRNA sequence that is transcribed from this gene?
 
# What is the ''exact'' mRNA sequence that is transcribed from this gene?
−
#* aaaagugguguucuuacuuacaaaagccguguaaagaggggucucacaauauuaacgccagcgucucaaccaaugcgaguaauggggcgacggcuauuccuuaaaaagcgcaguccauugcggguagcaaauagaguggcgagggaauaugca
+
#*aaaagugguguucuuacuuacaaaagccguguaaagaggggucucacaauauuaacgccagcgucucaaccaaugcgaguaauggggcgacggcuauuccuuaaaaagcgcaguccauugcggguagcaaauagaguggcgagggaauaugcaacgcgaaaaccacgccgaaucggcacacaaaagccucauuacacggcuuggacaaacaacgcuaaaucgcgcguuuagaaaugaauaaaugucuugaagccguaauagaacggccaaguuuaaugccaucacuauggggucuccuaaucuaccgguuucuucuguuauaacuuuacguuccauggcaagaacuuugcaacggauuaugguacaaggcgcaucucaaucuuuugccagugcaccaaugacguguguagaggccauuuuacgcguuuuugauguaggcguaggacugcccgcuguuucacugacaacuugacuggggcaugcuggacucguuuccggcguaacagaaggcaucagcgacuaacaaaauggcggacuacccgcuucucuuucuugcucauuuuccagccaaauuggccggaaaaauaaaaua
−
:::acgcgaaaaccacgccgaaucggcacacaaaagccucauuacacggcuuggacaaacaacgcuaaaucgcgcguuuagaaaugaauaaaugucuugaagccguaauagaacggccaaguuuaaugccaucacuauggggucuccuaaucuaccgguu
+
−
:::ucuucuguuauaacuuuacguuccauggcaagaacuuugcaacggauuaugguacaaggcgcaucucaaucuuuugccagugcaccaaugacguguguagaggccauuuuacgcguuuuugauguaggcguaggacugcccgcuguuucacuga
+
−
:caacuugacuggggcaugcuggacucguuuccggcguaacagaaggcaucagcgacuaacaaaauggcggacuacccgcuucucuuucuugcucauuuuccagccaaauuggccggaaaaauaaaaua
+
 
# What is the amino acid sequence that is translated from this mRNA?
 
# What is the amino acid sequence that is translated from this mRNA?
 +
#*Met A K E D N I E Met Q G T V L E T L P N T Met F R V E L E N G H V V T A H I S G K Met R K N Y I R I L T G D K V T V E L T P Y D L S K G R I V F R S R Stop
   −
NOTE: Answers not final
      
*All commands in one string
 
*All commands in one string
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Stack trace:
#0 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(480): _DiffEngine->_diag()
#1 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(291): _DiffEngine->_compareseq()
#2 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(175): _DiffEngine->diff_local()
#3 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(653): _DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(820): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(1240): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(1458): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(952): TableDiffFormatter->_changed()
#8 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(924): DiffFormatter->_block()
#9 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(765): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(655): DifferenceEngine->generateDiffBody()
#11 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(593): DifferenceEngine->getDiffBody()
#12 /apps/xmlpipedb/biodb/fall2013/includes/FeedUtils.php(147): DifferenceEngine->getDiff()
#13 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(303): FeedUtils::formatDiffRow()
#14 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(268): HistoryAction->feedItem()
#15 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(121): HistoryAction->feed()
#16 /apps/xmlpipedb/biodb/fall2013/includes/Action.php(541): HistoryAction->onView()
#17 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(427): FormlessAction->show()
#18 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(304): MediaWiki->performAction()
#19 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(536): MediaWiki->performRequest()
#20 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(446): MediaWiki->main()
#21 /apps/xmlpipedb/biodb/fall2013/index.php(59): MediaWiki->run()
#22 {main}