Ajvree Week 4
Class Notes:
[ct] at [at] at
[ct] :this can be c or t
[at] :this can be a or t
convert week 2 assignment to computer code by "counting" commands
bracket notation means find x "or" x
-10
cat infA-E.coli-K12.txt | sed "s/[ct]at[at]at/ HERE /g"
to find 2 HERE's
!! = rerun the command
HERE!! = HERE + rerun command
\ between exclamation points = put no importance to the exclamation points/ignore command
to add -35 spot, add another sed command
to add -10 or -35 box:
<minus35box>&</minus35box> etc
sed format doesn't know what slash is, must put another backslash before it
<minus35box>&<\/minus35box>
to find the 17 character endpoint, use periods
| sed "s/................. <minus10/<\/minus35box> &/g"
shortcut for repeated pattern: .{17}
if use this, after sed -r to allow shortcut
to mark the beginning
cat infA-E.coli-K12.txt | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed "s/................. <minus10/<\/minus35box> &/g" | sed "s/......<\/minus35box>/<minus35box>&/g"
put consensus sequence back in
cat infA-E.coli-K12.txt | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed "s/................. <minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/<minus35box>&/g"
start codon is closest to ribosome binding site
to find first atg after rbs
sed "s/<\/rbs>/&\n/g"
\n = new line
add # before s/<...
sed "2s/atg/<start_codon>&<\/start_codon> /1"
can replace g with a # to tell how many times something should happen
1.
Code:
cat infA-E.coli-K12.txt | sed "s/tttact/ <minus35box>&<\/minus35box> /g" | sed "s/cattat/ <minus10box>&<\/minus10box> /g" | sed "s/gagg/<rbs>&<\/rbs>/g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/<start_codon>&<\/start_codon> /1" | sed "2s/taa/<stop_codon>&<\/stop_codon> /1" | sed "s/<\/minus10box>/&\n/g" | sed "2s/./<tss>&<\/tss>/13" | sed "3s/aaaaggt/ <terminator>&/g" | sed "s/acctttt&..../<\/terminator>/g"
2.
Code:
sed "s/t/u/g" | rev
gcc aaa gaa gac aat att gaa atg caa ggt acc gtt ctt gaa acg ttg
mRNA:cgg uuu cuu cug uua caa cuu uac cca ugg caa gaa cuu ugc aac
3.
Amino acid sequence: R-F-L-L-L-Q-L-Y-P-W-Q-E-L-C-N
