Eyanosch Week 3

Erich Yanoschik

Week 3

In order to produce the complementary strands nucleotide sequence

cat sequence_file | sed "y/atgc/tacg/"

this follows the rule of y/<original characters>/<new characters>/

If sequence_file contains

agcggtatac

the output would be:

tcgccatatg

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.

Using Dondi's already available translated code we first need to translate the DNA into RNA, then make a way so that the code can read each trinucleotide sequence. If it reads the entire block of code then I won't be able to use the sed commands in Dr. Dondi's page.

cat sequence_file

• The file of nucleotide sequences

cat sequence_file | sed "s/t/u/g" 

• This will convert the Nucleotide sequence from DNA to RNA

cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" 

• This command repeats every 3 nucleotides and adds a space inbetween each codon

cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed

• by taking the codes from ~dondi/xmlpipedb/data directory in a file called genetic-code.sed, 64 chain commands are already taken care of.

cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g"

• Removing all the spaces in-between the Amino Acids

cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[actg]//g" 

• Removes any bases accidentally left

This reads for the +1 reading frame

cat sequence_file | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[actg]//g" 

• Reads for the +2 Reading Frame

cat sequence_file | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[actg]//g"

• Reads for the +3 Reading Frame

• The Negative reading frames

-1 reading frame:

cat sequence_file | sed "y/actg/tgac/" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[actg]//g"

-2 reading frame:

cat sequence_file | sed "y/actg/tgac/" | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[actg]//g"

-3 reading frame:

cat sequence_file | sed "y/actg/tgac/" | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[actg]//g"

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