Difference between revisions of "Kevin Wyllie Week 3"
From LMU BioDB 2015
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* As before, the -2 and -3 frames can be found by making a single adjustment to the pipe for the -1 frame. For the -2 frame: | * As before, the -2 and -3 frames can be found by making a single adjustment to the pipe for the -1 frame. For the -2 frame: | ||
| − | + | cat prokaryote.txt | sed "y/atgc/tacg/" | rev | '''sed "s/^.//g"''' | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | |
* And for the -3 frame: | * And for the -3 frame: | ||
| − | + | cat prokaryote.txt | sed "y/atgc/tacg/" | rev | '''sed "s/^..//g"''' | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | |
Revision as of 01:21, 20 September 2015
Contents
Complement of a Strand
- Shown in green: the following command is used to open the file (using prokaryote.txt as an example).
cat prokaryote.txt
- Shown in red: the following command is used to sequence the complementary strand (in the 5' -> 3' direction - thus the "rev" command).
cat prokaryote.txt | sed "y/atgc/tacg/" | rev
Reading Frames
The original sequence in the prokaryote.txt file will be assumed to be the top strand for this exercise.
+1, +2, and +3 Frames
- Shown in green: to separate the strand into codons (resulting in the +1 frame):
cat prokaryote.txt | sed "s/.../& /g"
- Shown in red: to convert to the mRNA sequence (treating the DNA stand as the mRNA-like strand):
cat prokaryote.txt | sed "s/.../& /g" | sed "y/t/u/"
- Shown in blue: to translate this mRNA sequence (yielding the +1 frame):
cat prokaryote.txt | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed
- For the +2 frame, the final pipe can be slightly altered:
cat prokaryote.txt | sed "s/^.//g" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed
- And similarly, for the +3 frame:
cat prokaryote.txt | sed "s/^..//g" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed
-1, -2, and -3 Frames
- For the -1 frame, open the file as usual, and then use the pipe from "Complement of a Strand" so that the commands after it will be applied to the complementary strand (instead of the original strand). Then, add the same pipe used for the +1 strand:
cat prokaryote.txt | sed "y/atgc/tacg/" | rev | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed
- As before, the -2 and -3 frames can be found by making a single adjustment to the pipe for the -1 frame. For the -2 frame:
cat prokaryote.txt | sed "y/atgc/tacg/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed
- And for the -3 frame:
cat prokaryote.txt | sed "y/atgc/tacg/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed
