|
|
| *Using <code>select count(*) from genenametype where type = 'ordered locus' and value ~ 'p?BCA[A-Z]?[0-9][0-9][0-9][A-Z]?[0-9]?[A-Z, a-z]?';</code>, it was verified that 337 OrderedLocusNames entries were present in B.cenocepacia_J2315_20151119_gmb3build5. | | *Using <code>select count(*) from genenametype where type = 'ordered locus' and value ~ 'p?BCA[A-Z]?[0-9][0-9][0-9][A-Z]?[0-9]?[A-Z, a-z]?';</code>, it was verified that 337 OrderedLocusNames entries were present in B.cenocepacia_J2315_20151119_gmb3build5. |
| *By looking at the data present in the genenametype table, it was found that the OrderedLocusName data was in the format of <code>BceJ2315_#####</code> | | *By looking at the data present in the genenametype table, it was found that the OrderedLocusName data was in the format of <code>BceJ2315_#####</code> |
− | ===Steps taken for further analysis=== | + | ===Steps taken for further analysis, conducted on 12/1=== |
| *The UniProt XML file was opened , via [http://www.firstobject.com/dn_editor.htm first object XML editor], in order to investigate and verify the location/nature of the OrderedLocusName data. | | *The UniProt XML file was opened , via [http://www.firstobject.com/dn_editor.htm first object XML editor], in order to investigate and verify the location/nature of the OrderedLocusName data. |
| *A data entry was selected and the related data was looked into: | | *A data entry was selected and the related data was looked into: |
|
|
| *A search query was conducted that consisted of <code>bcej2315 NOT gene:bca*</code>; this query, it was hoped, would show the number of gene entries that contained just an OrderedLocusName ID. | | *A search query was conducted that consisted of <code>bcej2315 NOT gene:bca*</code>; this query, it was hoped, would show the number of gene entries that contained just an OrderedLocusName ID. |
| [[File:UniProt_Results_2_12.1_GEN_BL14_20151201.png]] | | [[File:UniProt_Results_2_12.1_GEN_BL14_20151201.png]] |
Exception encountered, of type "Error"
[923e8412] /biodb/fall2015/index.php?diff=cur&oldid=7348&title=Blitvak_Week_14 Error from line 434 of /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php: Call to undefined function each()
Backtrace:
#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine->diag()
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine->compareSeq()
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter->changed()
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(111): DiffFormatter->block()
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine->generateTextDiffBody()
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine->generateContentDiffBody()
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine->getDiffBody()
#13 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(632): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(453): DifferenceEngine->showDiff()
#15 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(795): DifferenceEngine->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(506): Article->showDiffPage()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/ViewAction.php(44): Article->view()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): ViewAction->show()
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki->performAction()
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki->performRequest()
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki->main()
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
#23 {main}