https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Mpetredi_Week_3Mpetredi Week 3 - Revision history2026-05-02T20:54:48ZRevision history for this page on the wikiMediaWiki 1.20.3https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Mpetredi_Week_3&diff=1587&oldid=prevMpetredi: added journal entry category2013-09-13T05:09:51Z<p>added journal entry category</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category: Individual Homework]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category: Individual Homework]]</div></td></tr>
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</table>Mpetredihttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Mpetredi_Week_3&diff=1580&oldid=prevMpetredi: Added link back to my user page2013-09-13T04:59:04Z<p>Added link back to my user page</p>
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<tr><td colspan="2"> </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|'''Mitchell Petredis''']]==</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Compliment of a Strand==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Compliment of a Strand==</div></td></tr>
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</table>Mpetredihttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Mpetredi_Week_3&diff=1577&oldid=prevMpetredi: Added more answers and signature to individual assignment2013-09-13T04:53:54Z<p>Added more answers and signature to individual assignment</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==XMLPipeDB Match Practice==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==XMLPipeDB Match Practice==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># java -jar xmlpipedb-match-1.1.1.jar "GO:000916." < 493.P_falciparum.xml</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># java -jar xmlpipedb-match-1.1.1.jar "GO:000916." < 493.P_falciparum.xml</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#* There <del class="diffchange diffchange-inline">were </del>2 unique matches</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#* There <ins class="diffchange diffchange-inline">are </ins>2 unique matches<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#* Each unique match appears twice in the first line and once in the second line</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#* Each unique match appears twice in the first line and once in the second line<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"># java -jar xmlpipedb-match-1.1.1.jar  "\"James.*\"" < 493.P_falciparum.xml </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#*There are 2 unique matches.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#*The first line (james k.d.) has 8238 matches, and the second line james a.a. has 1 match.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#*"James" may refer to the person who sequenced all or a portion of falciparum.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#Use Match to count the occurrences of the pattern ATG in the hs_ref_GRCh37_chr19.fa file (this may take a while). Then, use grep and wc to do the same thing.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#* Match ATG results in 1 unique match appearing 830101 times</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#* grep and wc result in 502410 lines, 502410 words, and 35671048 characters</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#* These answers make sense because Match is only looking for a specific instance when ATG appears, which would make its value lower than the grep | wc combo. grep | wc cannot differentiate specific pieces of text and yields any occurrence when the pattern ATG comes up.</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[User:Mpetredi|Mpetredi]] ([[User talk:Mpetredi|talk]]) 21:53, 12 September 2013 (PDT)Mitchell Petredis</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Category: Individual Homework]]</ins></div></td></tr>
</table>Mpetredi
#cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
#cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
−
#
+
#cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | sed "s^.//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
+
#cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | sed "s^..//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed