Stephen Louie Week 4

Transcription and Translation “Taken to the Next Level”

1. Input: cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <-10box> & <\/-10box> /g" | sed "s/................. <-10box>/ <\/-35box> &/g" |sed "s/...... <\/-35box>/ <-35box> &/g" | sed "s/ <-10box> ...... <\/-10box> ...../& <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> .{3}*t[ag][ag]/& <\/stop_codon> /g" | sed "2s/... <\/stop_codon>/ <stop_codon> &/g" | sed "2s/aaaaggt/ <terminator> &/g" | sed "2s/tttt..../& <\/terminator> /2" Output:ttttcaccacaagaatgaatgttttcggcacatttctccccagagtgttataattgcggtcgcagagttggttacgctcattaccccgctgccgataaggaatttttcgcgtcaggtaacgcccatcgtttatctcaccgctcccttatacgttgcgcttttggtgcggcttagccgtgtgttttcggagtaatgtgccgaacctgtttgttgcgatttagcgcgcaaatc <-35box> tttact </-35box> tatttacagaacttcgg <-10box> cattat </-10box> cttgc <tss> c </tss> ggttcaaattacggtagtgatacccca <rbs> gagg </rbs> attag <start_codon> atg </start_codon> gccaaagaagacaatattgaaatgcaaggtaccgttcttgaaacgttgcctaataccatgttccgcgtagagttagaaaacggtcacgtggttactgcacacatctccggtaaaatgcgcaaaaactacatccgcatcctgacgggcgacaaagtgactgttgaactgaccccgtacgacctgagcaaaggccgcattgtcttccgtagtcgc <stop_codon> tga </stop_codon> ttgttttaccgcctgatgggcgaagagaaagaacgagt <terminator> aaaaggtcggtttaaccggcctttttatt </terminator> ttat
2. Input:cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <-10box> & <\/-10box> /g" | sed "s/................. <-10box>/ <\/-35box> &/g" |sed "s/...... <\/-35box>/ <-35box> &/g" | sed "s/ <-10box> ...... <\/-10box> ...../& <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> .{3}*t[ag][ag]/& <\/stop_codon> /g" | sed "2s/... <\/stop_codon>/ <stop_codon> &/g" | sed "2s/aaaaggt/ <terminator> &/g" | sed "2s/tttt..../& <\/terminator> /2" | sed "y/atcg/uagc/" Output:gccaaguuuaaugccaucacuauggggucuccuaaucuaccgguuucuucuguuauaacuuuacguuccauggcaagaacuuugcaacggauuaugguacaaggcgcaucucaaucuuuugccagugcaccaaugacguguguagaggccauuuuacgcguuuuugauguaggcguaggacugcccgcuguuucacugacaacuugacuggggcaugcuggacucguuuccggcguaacagaaggcaucagcgacuaacaaaauggcggacuacccgcuucucuuucuugcucauuuuccagccaaauuggccggaaaaauaa
3. Input:cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <-10box> & <\/-10box> /g" | sed "s/................. <-10box>/ <\/-35box> &/g" |sed "s/...... <\/-35box>/ <-35box> &/g" | sed "s/ <-10box> ...... <\/-10box> ...../& <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> .{3}*t[ag][ag]/& <\/stop_codon> /g" | sed "2s/... <\/stop_codon>/ <stop_codon> &/g" | sed "2s/aaaaggt/ <terminator> &/g" | sed "2s/tttt..../& <\/terminator> /2" | sed ':a;N;$!ba;s/\n//g' | sed "s/ atg <\/start_codon> /\natg/g" |sed "s/ <stop_codon> tga/tga\n/g" |sed 1D |sed 2D | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed

Output:M A K E D N I E M Q G T V L E T L P N T M F R V E L E N G H V V T A H I S G K M R K N Y I R I L T G D K V T V E L T P Y D L S K G R I V F R S R - Slouie (talk) 22:17, 19 September 2013 (PDT)