Kmeilak Week 4

Week 4

Transcription and Translation “Taken to the Next Level”

1.

cat infA-E.coli-K12.txt  | sed "s/cat[at]at/ <minus10box> & <\/minus10box> /g" | sed -r "s/.{17} <minus10box>/ <\/minus35box> &/g" | sed -r "s/.{6} <\/minus35box>/ <minus35box> &/g" | sed -r "s/ <minus10box> .{6} <\/minus10box> .{5}/& <tss> /g" | sed "s/ <tss> ./& <\/tss> /g" | sed "s/gagg/ <rbs> & <\/rbs>\n/g" | sed "2s/atg/ <start_codon> & <\/start_codon> /1" | sed -r "2s/<\/start_codon> ...*t[ag][ag]/& <\/stop_codon> /g" | sed "2s/... <\/stop_codon>/ <stop_codon> &/g" | sed "2s/aaaaggt/ <terminator> &/g" | sed "2s/tttt..../& <\/terminator> /2"

• sequence of -35 box

tttact

• sequence of -10 box

cattat

• transcription start site base pair

c

• sequence of ribosome binding site

gagg

• start codon

atg

• stop codon

tga

• terminator sequence

aaaaggtcggtttaaccggcctttttatt