sed “s/[acug]//g”

  sed “s/[acug]//g”

I then proceeded with the rest of the commands so the list of commands looked like this:

I then proceeded with the rest of the commands so the list of commands looked like this:

  cat infA-E.coli-K12.txt | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed “s/[acug]//g”

  cat infA-E.coli-K12.txt | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed “s/[acug]//g”

For the -2 and -3 reading frames I just needed to add the same command sed "s/^.//g" (for -2) and sed "s/^..//g" (for frame -3), with each (.) indicating the deletion of one nucleotide. I inserted this right after reversing the sequence so that it did not mess with the translated sequence, which would affect how the sequence was transcribed later on in the set. For -2 the command set was  

For the -2 and -3 reading frames I just needed to add the same command sed "s/^.//g" (for -2) and sed "s/^..//g" (for frame -3), with each (.) indicating the deletion of one nucleotide. I inserted this right after reversing the sequence so that it did not mess with the translated sequence, which would affect how the sequence was transcribed later on in the set. For -2 the command set was  

cat infA-E.coli-K12.txt | sed "y/atcg/tagc/" | rev | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g"

cat infA-E.coli-K12.txt | sed "y/atcg/tagc/" | rev | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g"

For the -3 reading frame the command set was  

For the -3 reading frame the command set was  

cat infA-E.coli-K12.txt | sed "y/atcg/tagc/" | rev | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g"

cat infA-E.coli-K12.txt | sed "y/atcg/tagc/" | rev | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g"

I checked these sequences using the ExPASy Translate tool from the Bioinformatics Resource Portal and verified that they worked correctly.  

I checked these sequences using the ExPASy Translate tool from the Bioinformatics Resource Portal and verified that they worked correctly.  

#* How many unique matches are there? '''3'''

#* How many unique matches are there? '''3'''

#* How many times does each unique match appear? '''The first appears 113 times, the second appears 1,100 times, and the third appears 1,371 times.'''

#* How many times does each unique match appear? '''The first appears 113 times, the second appears 1,100 times, and the third appears 1,371 times.'''