I opened up terminal, and used the ssh command to get into dondi's directory: ~dondi/xmlpipedb/data.  In there I got access to infA-E.coli-K12.txt which is the nucleotide sequence I will be using for this assignment.   

I opened up terminal, and used the ssh command to get into dondi's directory: ~dondi/xmlpipedb/data.  In there I got access to infA-E.coli-K12.txt which is the nucleotide sequence I will be using for this assignment.   

# Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):

* Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):

* -35 box of the promoter

* -35 box of the promoter

**As shown in class I used the sed command to get the first occurrence of the minus 35 strand in the sequence:

**As shown in class I used the sed command to get the first occurrence of the minus 35 strand in the sequence:

** 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>

** 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>

*terminator

*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>

* And so, finally, it is all marked up.  However I'm not quite done yet, I need to get rid of all the new lines I created.  In order to do this I used this command:  sed ':a;N;$!ba;s/\n//g' (from wiki), so the final output is as follows.

* And so, finally, it is all marked up.  However I'm not quite done yet, I need to get rid of all the new lines I created.  In order to do this I used this command:  sed ':a;N;$!ba;s/\n//g' (from wiki), so the final output is as follows.

#*(a)<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" | sed ':a;N;$!ba;s/\n//g' </code>

*(a)