https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Laurmagee%3A_Week_4 Laurmagee: Week 4 - Revision history 2026-04-30T06:33:20Z Revision history for this page on the wiki MediaWiki 1.20.3  
==Added Stop Codon==
 
==Added Stop Codon==
 
#cat [file] | sed "s/<\/start_codon>/&\n/g" | sed "s/.../&/g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1"  
 
#cat [file] | sed "s/<\/start_codon>/&\n/g" | sed "s/.../&/g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1"  
−
#cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/ <\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed "s/<\/start_codon>/&\n/g" | sed "s/.../& /g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1"  
+
#cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/ <\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed "s/<\/start_codon>/&\n/g" | sed "s/.../& /g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1" | sed "4s/tga/ <stop_codon>&<\/stop_codon>/1" |  sed "4s/taa/ <stop_codon>&<\/stop_codon>/1"  
    
==Transition Start Site==
 
==Transition Start Site==
 
#cat [file] | sed "s/.{12} <minus10/ <tss>&<\/tss>/g"
 
#cat [file] | sed "s/.{12} <minus10/ <tss>&<\/tss>/g"
−
#cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/ <\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed "s/<\/start_codon>/&\n/g" | sed "s/.../& /g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1" | sed "s/.{12} <minus10/ <tss>&<\/tss>/g"
+
#cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/ <\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed "s/<\/start_codon>/&\n/g" | sed "s/.../& /g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1" | sed "4s/tga/ <stop_codon>&<\/stop_codon>/1" |  sed "4s/taa/ <stop_codon>&<\/stop_codon>/1" | sed -r "s/.{12} <minus10/ <tss>&<\/tss>/g"
 
   
 
   
 
==Terminator==
 
==Terminator==
 
#cat [file] | sed "s/aaaaggt .{4}/ <terminator>&<\/terminator>/g"
 
#cat [file] | sed "s/aaaaggt .{4}/ <terminator>&<\/terminator>/g"
Unexpected non-MediaWiki exception encountered, of type "Error"
Error: Call to undefined function each() in /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php:374
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(895): 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}