Difference between revisions of "Ajvree Week 4"

Revision as of 18:53, 19 September 2013

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.

• cat infA-E.coli-K12.txt | sed "s/tt[gt]ac[at]<\/minus35box>&<\/minus35box> /g"

sequence: tttact

• cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g"

sequence is cattat

• cat infA-E.coli-K12.txt | sed "

Code so far: 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"

Updated:

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"