Gleis Week 4

"Taken to the Next Level"

a) ttttcaccacaagaatgaatgttttcggcacatttctccccagagtgttataattgcg

gtcgcagagttggttacgctcattaccccgctgccgataaggaatttttcgc gtcaggtaacgcccatcgtttatctcaccgctcccttatacgttgcgcttttggtgcggcttagccgtgtgttttcggagtaatgtgccgaacctgtttgttgcgatttagcgcgcaaatc <minus35box>tttact</minus35box> tatttacagaacttcgg <minus10box>cattat</minus10box> cttgcc<tss> g</tss> gttcaaattacggtagtgatacccca <rbs>gagg</rbs> attag <start_codon>atg</start_codon> gccaaagaagacaatat <stop_codon>tga</stop_codon> aatgcaaggtaccgttcttgaaacgttgcctaataccatgttc cgcgtagagttagaaaacggtcacgtggttactgcacacatctccggtaaaatgcgcaaaaactacatccgcatcctgacgggcgacaaagtga ctgttgaactgaccccgtacgacctgagcaaaggccgcattgtcttccgtagtcgctgattgttttaccgcctgatgggcgaagagaaagaacgagtaaaaggtcggtttaaccg <terminator>gcctttttatt</terminator> tta

b) cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/.../&/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed -r "s/.{26} <rbs/<\/tss> &/g" | sed -r "s/.<\/tss/<tss> &/g" | sed "2s/gcctttt..../ <terminator>&<\/terminator> /g" | sed "2s/t[ag][ag]/ <stop_codon>&<\/stop_codon> /g"

2 a)gguucaaauuacgguagugauaccccagaggauauggccaaagaagacaauauugaaaugcaagguaccguucuugaaacguugccuaauaccau guuccgcguagaguuagaaaacggucacgugguuacugcacaca ucuccgguaaaaugcgcaaaaacuacauccgcauccugacgggcgacaaagugacuguugaacug accccguacgaccugagcaaaggccgcauugucuuccguagucgcugauuguuuuaccgccugaugggcgaagagaaagaacgaguaaaaggucgguuuaaccggccuuuuuauu

b) cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/.../&/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed -r "s/.{26} <rbs/<\/tss> &/g" | sed -r "s/.<\/tss/<tss> &/g" | sed "2s/gcctttt..../ <terminator>&<\/terminator> /g" | sed "2s/t[ag][ag]/ <stop_codon>&<\/stop_codon> /2" | sed "s/t/u/g"

3 a) MPKTTI b) cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/.../&/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed -r "s/.{26} <rbs/<\/tss> &/g" | sed -r "s/.<\/tss/<tss> &/g" | sed "2s/gcctttt..../ <terminator>&<\/terminator> /g" | sed "2s/t[ag][ag]/ <stop_codon>&<\/stop_codon> /2" | sed "s/t/u/g" | sed -f genetic-code.sed