https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Kevinmcgee_Week_3 Kevinmcgee Week 3 - Revision history 2026-04-15T18:46:05Z Revision history for this page on the wiki MediaWiki 1.20.3 https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Kevinmcgee_Week_3&diff=1464&oldid=prev Kevinmcgee: Added XML match homework 2013-09-12T18:40:45Z <p>Added XML match homework</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 18:40, 12 September 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 13:</td> <td colspan="2" class="diff-lineno">Line 13:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; -3 seq_file | sed &quot;y/actg/tgac/&quot; | rev | sed &quot;s/^..//g&quot; | sed &quot;s/.../&amp; /g&quot; | sed &quot;s/t/u/g&quot; | sed -f genetic-code.sed</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; -3 seq_file | sed &quot;y/actg/tgac/&quot; | rev | sed &quot;s/^..//g&quot; | sed &quot;s/.../&amp; /g&quot; | sed &quot;s/t/u/g&quot; | sed -f genetic-code.sed</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 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;">==XMLPipeDB Match Practice==</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;">#What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?</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;">:*2 unique matches</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;">:*First match occurred twice, second match occured once.</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;">:* There appears to be multiple references to this in the doccument. It appears to be a specific alignment on a protein sequence of 493.P-Falciparum</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;">#What Match command tallies the occurrences of the pattern \&quot;James.*\&quot; in the 493.P_falciparum.xml file?</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;">:*2 Unique matches</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;">:*First match occurred 8238 times, second match occurred 1 time.</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;">:*When I typed in the command grep &quot;\James.*\&quot;&quot;, it told me that it was a persons name. By looking at the title and noticing the file is copyrighted, I believe that it is safe to assume that James K.D. is the name of an author of a scientific article.</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;">#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">&#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;">:* Match brought back 830,101 matches</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;">:* grep and wc gave me 502,401 lines, 502,401 words and 35671048 letters</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;">:* It makes sense that grep and wc had less matches because they cannot account for multiple matches on the same line.</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>[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 11:14, 12 September 2013 (PDT)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 11:14, 12 September 2013 (PDT)</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: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> Kevinmcgee  +
==Genetic Code By Computer==
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