Difference between revisions of "Ksherbina Week 4"
From LMU BioDB 2013
(→Transcription and Translation "Taken to the Next Level": Altered the piped sequence of text to include commands to tag the stop codon.) |
(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.) |
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#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} < | + | 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
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| 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"
