==Transcription and Translation "Taken to the Next Level"==

==Modifying the Gene Sequence==

To start this assignment I began by opening Terminal on my laptop. I entered  

To start this assignment I began by opening Terminal on my laptop. I entered  

I began by using grep to find the potential -35 box and -10 box because grep highlights the searched pattern in red. I simply entered

I began by using grep to find the potential -35 box and -10 box because grep highlights the searched pattern in red. I simply entered

cat infA-E.coli-K12.txt | grep "tt[gt]ac[at]"

  cat infA-E.coli-K12.txt | grep "tt[gt]ac[at]"

which gave me two possible answers for the -35 box, '''tttact''' and '''tttaca''', both of which fit the pattern. Now it was a matter of finding out which one was the correct one. I also searched for the -10 box using

which gave me two possible answers for the -35 box, '''tttact''' and '''tttaca''', both of which fit the pattern. Now it was a matter of finding out which one was the correct one. I also searched for the -10 box using

cat infA-E.coli-K12.txt | grep "[ct]at[at]at"

  cat infA-E.coli-K12.txt | grep "[ct]at[at]at"

which also revealed two potential sites at '''tataat''' and '''cattat'''. I realized that in order to find out which sequences were the correct ones I needed to visualize them both together, but grep doesn't do this, so instead I used sed. To do this, I entered the sed commands as a pipe, and added three space on either side of each occurrence of the consensus sequences (both -35 and -10) in the file to make the sequences more visible.. This is done by adding  sed "s/<pattern>/& /g" where <pattern> is what I wish to find and each space after the "&" sign is what I wished to add to each side of the pattern (instructions found [[Introduction to the Command Line | here]]). The pipe looked like this:

which also revealed two potential sites at '''tataat''' and '''cattat'''. I realized that in order to find out which sequences were the correct ones I needed to visualize them both together, but grep doesn't do this, so instead I used sed. To do this, I entered the sed commands as a pipe, and added three space on either side of each occurrence of the consensus sequences (both -35 and -10) in the file to make the sequences more visible.. This is done by adding  sed "s/<pattern>/& /g" where <pattern> is what I wish to find and each space after the "&" sign is what I wished to add to each side of the pattern (instructions found [[Introduction to the Command Line | here]]). The pipe looked like this: