Bklein7 Week 4
From LMU BioDB 2015
Contents
Transcription and Translation "Taken to the Next Level"
- 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 box of the promoter
... <minus35box>...</minus35box> ...
- -10 box of the promoter
... <minus10box>...</minus10box> ...
- transcription start site
... <tss>...</tss> ...
- ribosome binding site
... <rbs>...</rbs> ...
- start codon
... <start_codon>...</start_codon> ...
- stop codon
... <stop_codon>...</stop_codon> ...
- terminator
... <terminator>...</terminator> ...
- -35 box of the promoter
- What is the exact mRNA sequence that is transcribed from this gene?
- What is the amino acid sequence that is translated from this mRNA?
Preliminary Code
sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^. {17}/&<minus10box>/g" | sed "s/<minus10box>....../&<\/minus10box/g" | sed -r "s/<\/minus10box>.{11}/&<tss>/g" | sed "s/<tss>./&<\/tss/g" | sed "s/gagg/<rbs>&<\/rbs>\n/g" | sed "3s/atg/<start_codon>&<\/start_codon>\n/1" | sed "s/aaaaggt/\n<terminator>&/g" | sed - r "s/aaaaggt.*gcctttt.{4}/&<\/terminator>/g" | sed "4s/.../& /g" | sed -r "4s/taa|tag|tga/<stop_codon>&<\/stop_codon>/g" | sed "4s/ //g" | sed ':a;N;$!ba;s/\n//g'
- String together redundant sed commands with ; or find a way to make them more compact
- Verify when the terminator sequence starts
- Is there a way to count backwards in a line with sed? or so replace only the last instance that matches? previous experiments
- sed "s/x.*$/y/g" - does not work, wild card overtakes the last instance
- sed "s/x/y/1$" - does not work
- answer: use rev commands!
Links
- User Page: Brandon Klein
- Team Page: The Class Whoopers
Assignments Pages
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