Difference between revisions of "Lena Week 4"
From LMU BioDB 2013
(compiled some answers to week 4 questions) |
(noted unsure about stop codon) |
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# Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag): | # Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag): | ||
| + | |||
#* -35 and -10 box of the promoter | #* -35 and -10 box of the promoter | ||
| + | |||
#** 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" | #** 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" | ||
| + | |||
#* transcription start site | #* transcription start site | ||
| + | |||
#**cat infA-E.coli-K12.txt | sed "2s/atg/<tss>&<\/tss> /1" | #**cat infA-E.coli-K12.txt | sed "2s/atg/<tss>&<\/tss> /1" | ||
| + | |||
#* ribosome binding site | #* ribosome binding site | ||
| + | |||
#**cat infA-E.coli-K12.txt | sed "s/gagg/ <rbs>&<\/rbs> /g" | #**cat infA-E.coli-K12.txt | sed "s/gagg/ <rbs>&<\/rbs> /g" | ||
| + | |||
#*start codon | #*start codon | ||
| + | |||
#**cat infA-E.coli-K12.txt | sed "2s/atg/ <start_codon>&<\/start_codon> /g" | #**cat infA-E.coli-K12.txt | sed "2s/atg/ <start_codon>&<\/start_codon> /g" | ||
| − | #* stop codon | + | |
| + | #* stop codon (*Note: not final answer) | ||
| + | |||
#**cat infA-E.coli-K12.txt | sed "2s/t[ag][ag]/ <stop_codon>&<\/stop_codon> /2" | #**cat infA-E.coli-K12.txt | sed "2s/t[ag][ag]/ <stop_codon>&<\/stop_codon> /2" | ||
| + | |||
#*terminator | #*terminator | ||
| + | |||
#**cat infA-E.coli-K12.txt | sed "s/aaaaggt...........gcctttt..../ <terminator>&<\/terminator> /g" | #**cat infA-E.coli-K12.txt | sed "s/aaaaggt...........gcctttt..../ <terminator>&<\/terminator> /g" | ||
| + | |||
# What is the ''exact'' mRNA sequence that is transcribed from this gene? | # What is the ''exact'' mRNA sequence that is transcribed from this gene? | ||
| + | |||
# What is the amino acid sequence that is translated from this mRNA? | # What is the amino acid sequence that is translated from this mRNA? | ||
Revision as of 18:42, 19 September 2013
- Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):
- -35 and -10 box of the promoter
- 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"
- transcription start site
- cat infA-E.coli-K12.txt | sed "2s/atg/<tss>&<\/tss> /1"
- ribosome binding site
- cat infA-E.coli-K12.txt | sed "s/gagg/ <rbs>&<\/rbs> /g"
- start codon
- cat infA-E.coli-K12.txt | sed "2s/atg/ <start_codon>&<\/start_codon> /g"
- stop codon (*Note: not final answer)
- cat infA-E.coli-K12.txt | sed "2s/t[ag][ag]/ <stop_codon>&<\/stop_codon> /2"
- terminator
- cat infA-E.coli-K12.txt | sed "s/aaaaggt...........gcctttt..../ <terminator>&<\/terminator> /g"
- What is the exact mRNA sequence that is transcribed from this gene?
- What is the amino acid sequence that is translated from this mRNA?
- All commands in one string
- 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_codon>&<\/start_codon> /1" | sed "2s/t[ag][ag]/ <stop_codon>&<\/stop_codon> /2" | sed "s/aaaaggt...........gcctttt..../ <terminator>&<\/terminator> /g" | sed "2s/atg/<tss>&<\/tss> /1"
