** The stop codon requires I find one of three possible three character sequences.  At first I tried using brackets: "t[ag][ag]", but I soon found out that that yielded too many results.  There are only three stop codons and the brackets give me 4 unique codons.  So into the wiki I went, and realized I could use a vertical bar to separate three unique codons, and search for them.  The problem however, was that this did not work.  After being stumped for awhile I realized that before I piped to that command I needed to break up the line into sets of 3, just like I did in the week 3 assignment.  As a result I got this command: <code> cat infA-E.coli-K12.txt | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box>\n/1" | sed -r "2s/^.{17}/&\n/g" | sed -r "3s/[ct]at[at]at/<minus10box>&<\/minus10box>\n/1" | sed -r "4s/^.{5}/&\n/g" | sed "5s/^./<tss>&<\/tss>\n/g" | sed "6s/gagg/<rbs>&<\/rbs>\n/1" | sed "7s/atg/<start_codon>&<\/start_codon>\n/1" | sed "8s/.../& /g"| sed -r "8s/tag|tga|taa/<stop_codon>&<\/stop_codon>/1"

** The stop codon requires I find one of three possible three character sequences.  At first I tried using brackets: "t[ag][ag]", but I soon found out that that yielded too many results.  There are only three stop codons and the brackets give me 4 unique codons.  So into the wiki I went, and realized I could use a vertical bar to separate three unique codons, and search for them.  The problem however, was that this did not work.  After being stumped for awhile I realized that before I piped to that command I needed to break up the line into sets of 3, just like I did in the week 3 assignment.  As a result I got this command: <code> cat infA-E.coli-K12.txt | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box>\n/1" | sed -r "2s/^.{17}/&\n/g" | sed -r "3s/[ct]at[at]at/<minus10box>&<\/minus10box>\n/1" | sed -r "4s/^.{5}/&\n/g" | sed "5s/^./<tss>&<\/tss>\n/g" | sed "6s/gagg/<rbs>&<\/rbs>\n/1" | sed "7s/atg/<start_codon>&<\/start_codon>\n/1" | sed "8s/.../& /g"| sed -r "8s/tag|tga|taa/<stop_codon>&<\/stop_codon>/1"

</code>

</code>

* terminator <pre>... <terminator>...</terminator> ...</pre>

* terminator

** The first part of the terminator hairpin is: <code> aaaaggt </code>, which means, abiding by the rules of the terminator provided to us, that the first half bonds with <code> gcctttt </code>.  So now the trick is to grab the correct terminator sequence.  I ended up breaking the terminator command into two different commands.  I used one to insert the first tag, and the second one to insert the second tag.  I did this because I wasn't sure how long the sequence would be between the two hairpin sequences. This is what I got to capture the terminator sequence: <code> cat infA-E.coli-K12.txt | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box>\n/1" | sed -r "2s/^.{17}/&\n/g" | sed -r "3s/[ct]at[at]at/<minus10box>&<\/minus10box>\n/1" | sed -r "4s/^.{5}/&\n/g" | sed "5s/^./<tss>&<\/tss>\n/g" | sed "6s/gagg/<rbs>&<\/rbs>\n/1" | sed "7s/atg/<start_codon>&<\/start_codon>\n/1" | sed "8s/.../& /g"| sed -r "8s/tag|tga|taa/<stop_codon>&<\/stop_codon>/1" | sed "8s/ //g" | sed "8s/aaaaggt/<terminator>&/g" | sed -r "8s/gcctttt..../&<\/terminator>/g" </code>

** The first part of the terminator hairpin is: <code> aaaaggt </code>, which means, abiding by the rules of the terminator provided to us, that the first half bonds with <code> gcctttt </code>.  So now the trick is to grab the correct terminator sequence.  I ended up breaking the terminator command into two different commands.  I used one to insert the first tag, and the second one to insert the second tag.  I did this because I wasn't sure how long the sequence would be between the two hairpin sequences. This is what I got to capture the terminator sequence: <code> cat infA-E.coli-K12.txt | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box>\n/1" | sed -r "2s/^.{17}/&\n/g" | sed -r "3s/[ct]at[at]at/<minus10box>&<\/minus10box>\n/1" | sed -r "4s/^.{5}/&\n/g" | sed "5s/^./<tss>&<\/tss>\n/g" | sed "6s/gagg/<rbs>&<\/rbs>\n/1" | sed "7s/atg/<start_codon>&<\/start_codon>\n/1" | sed "8s/.../& /g"| sed -r "8s/tag|tga|taa/<stop_codon>&<\/stop_codon>/1" | sed "8s/ //g" | sed "8s/aaaaggt/<terminator>&/g" | sed -r "8s/gcctttt..../&<\/terminator>/g" </code>