sed "8s/atg/<start_codon>&<\/start_codon>\n/1" |
 
  sed "8s/atg/<start_codon>&<\/start_codon>\n/1" |
 
  sed "9s/.../& /" |
 
  sed "9s/.../& /" |
  sed "9s/tag|tga|taa/<stop_codon>&<\/stop_codon>/" |
+
  sed -r "9s/tag|tga|taa/<stop_codon>&<\/stop_codon>/" |
 
  sed "9s/ //" |
 
  sed "9s/ //" |
 
  sed "9s/<stop_codon>/ &/" |
 
  sed "9s/<stop_codon>/ &/" |
 
=== mRNA transcribed from the gene ===
 
=== mRNA transcribed from the gene ===
 
In order to get the mRNA strand from the DNA strand, we first have to extract the section of the DNA strand that is actually read from the rest of it. I was thinking of using some regex patterns for extracting the necessary strand, but couldn't think of a way to isolate the tags on the inside and still keep the strands I wanted to transcribe. I ended up looking through another students' methods and found that Nicole Anguiano's method is a lot more efficient than anything I thought of so borrowed her process. However, I did notice that here method only switched the t's with the u's. The correct way of translating DNA into mRNA would be to switch ALL bases with their corresponding mRNA base:
 
In order to get the mRNA strand from the DNA strand, we first have to extract the section of the DNA strand that is actually read from the rest of it. I was thinking of using some regex patterns for extracting the necessary strand, but couldn't think of a way to isolate the tags on the inside and still keep the strands I wanted to transcribe. I ended up looking through another students' methods and found that Nicole Anguiano's method is a lot more efficient than anything I thought of so borrowed her process. However, I did notice that here method only switched the t's with the u's. The correct way of translating DNA into mRNA would be to switch ALL bases with their corresponding mRNA base:
Exception encountered, of type "Error"
[1ad63c28] /biodb/fall2015/index.php?diff=1984&oldid=1978&title=Troque_Week_4 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(82): 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}