Laurmagee: Week 3

Complement of a Strand

• The appropriate processing commands are the following: cat sequence_file | sed "y/atgc/tacg/"
• This will turn a nucleotide sequence, "agcggtatac", into "tcgccatatg", it's compliment.

Reading Frames

1. First Reading Frame (+1)
   • cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
2. Second Reading Frame (+2)
   • cat sequence_file | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
3. Third Reading Frame (+3)
   • cat sequence_file | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
4. Fourth Reading Frame (-1)
   • rev sequence_file | sed "y/atgc/tacg/" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
5. Fifth Reading Frame (-2)
   • rev sequence_file | sed "y/atgc/tacg/" | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
6. Sixth Reading Frame (-3)
   • rev sequence_file | sed "y/atgc/tacg/" | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed