==== Reading Frames ====
 
==== Reading Frames ====
 
Write ''6'' sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.
 
Write ''6'' sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.
−
*To tackle this problem, start by crafting the simplest sequence of commands that will carry out the central dogma by translating DNA sequences to amino acid sequences. This command sequence will serve as the backbone from which all 6 reading frame sequences are built. Incidentally, this code will also align with that necessary to transcribe the ''+1 reading frame''.
+
*To tackle this problem, start by crafting the simplest sequence of commands that will carry out the central dogma by translating DNA sequences to amino acid sequences. This command sequence will serve as the "backbone" from which all 6 reading frame sequences are built. Incidentally, this code will also align with that necessary to transcribe the ''+1 reading frame''.
 
*#Begin with a cat command to view a text file with a DNA sequence
 
*#Begin with a cat command to view a text file with a DNA sequence
 
*#*cat ''sequence_file''
 
*#*cat ''sequence_file''
    
*'''-1 Reading Frame'''
 
*'''-1 Reading Frame'''
 +
**The "backbone" command sequence from above will have to be slightly altered for the negative reading frames to account for the reading of a complimentary, antiparallel strand of DNA
 +
**#Begin with the code from the +1 reading frame
 +
**#*cat ''sequence_file'' | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"
 +
**#Add the sed command from the "Compliment of a Strand" section above at the beginning of this sequence. This will yield the DNA sequence complimentary to that which we were originally working with
 +
**#*cat ''sequence_file'' | sed "y/atcg/tagc/" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"
 +
**#Add a rev command after the code has been transcribed to the complimentary mRNA. This accounts for the fact that the genetic code is read in the 5' to 3' direction. With this final change, the command sequence will now translate the DNA sequence within the -1 reading frame:
 +
cat ''sequence_file'' | sed "y/atcg/tagc/" | sed "s/t/u/g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" |
 +
sed "s/ //g"
 
*'''-2 Reading Frame'''
 
*'''-2 Reading Frame'''
 +
**As in the positive reading frames, alter the -1 reading frame code to include a sed command for the deletion of the first character of the text file (i.e. nucleotide) prior to division into triplets:
 +
cat ''sequence_file'' | sed "y/atcg/tagc/" | sed "s/t/u/g" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed |
 +
sed "s/[atcg]//g" | sed "s/ //g"
 
*'''-3 Reading Frame'''
 
*'''-3 Reading Frame'''
Exception encountered, of type "Error"
[64709d4a] /biodb/fall2015/index.php?diff=next&oldid=1281&title=User%3ABklein7 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}