Difference between revisions of "Ksherbina Week 4"
From LMU BioDB 2013
(Modified the part of the piped sequence of text that tag this stop codon. Added to the pipe sequence of text commands to find the transcription start site and the terminator.) |
(→Transcription and Translation "Taken to the Next Level": Changed how the piped text is displayed.) |
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| Line 5: | Line 5: | ||
#The piped sequence of text to tag the ''infA'' gene in ''E. coli'' K12: | #The piped sequence of text to tag the ''infA'' gene in ''E. coli'' K12: | ||
| − | + | cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10box/<\/minus35b ox> &/g" | sed "s/tt[gt]ac[at]<\/minus35box> / <minus35box>&/g" | sed -r "s/\/minus10box> .{6}/&<\/tss> /g" | sed "s/.<\/tss> / <tss>&/g" | sed "s/gagg/ <rbs>&<\/rb s>/g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed -r "2s/<\/start_codon> .{3}*t[ag][ag]/&<\/stop_codon> /g" | sed "s/...<\/stop_c odon> / <stop_codon>&/g" | sed "2s/aaaaggt/ <terminator>&/g" | sed "2s/gcctttt/&<\/terminator> /g" | |
<!-- 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/atg/&<\/START>/1" | <!-- 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/atg/&<\/START>/1" | ||
Revision as of 05:15, 20 September 2013
| Assignment Description | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 15 |
| Class Journal | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | |||||
| Individual Journal | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 |
| Other | Week 5: Database Wiki |
| Final Project | Team H(oo)KD Project Page | Journal Club Presentation | Project Individual Journal |
Transcription and Translation "Taken to the Next Level"
- The piped sequence of text to tag the infA gene in E. coli K12:
cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10box/<\/minus35b ox> &/g" | sed "s/tt[gt]ac[at]<\/minus35box> / <minus35box>&/g" | sed -r "s/\/minus10box> .{6}/&<\/tss> /g" | sed "s/.<\/tss> / <tss>&/g" | sed "s/gagg/ <rbs>&<\/rb s>/g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed -r "2s/<\/start_codon> .{3}*t[ag][ag]/&<\/stop_codon> /g" | sed "s/...<\/stop_c odon> / <stop_codon>&/g" | sed "2s/aaaaggt/ <terminator>&/g" | sed "2s/gcctttt/&<\/terminator> /g"
