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Revision as of 22:04, 15 September 2015
Contents
The Genetic Code, by Computer
Connect to the my.cs.lmu.edu workstation as shown in class and do the following exercises from there.
For this exercise, I performed the following series of commands to prepare for the assignment.
ssh my.cs.lmu.edu -l nanguia1 mkdir biodb cat >"sequence_file.txt" agcggtatac cd biodb mkdir week3 mv sequence_file.txt biodb/week3 cd ~dondi/xmlpipedb/data cp genetic-code.sed ~nanguia1/biodb/week3 cd ~nanguia1/biodb/week3
Complement of a Strand
Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.
On a sequence_file.txt file containing the sequence "agcggtatac", the command and output was as follows:
cat sequence_file.txt | sed "y/atgc/tacg/" tcgccatatg
Reading Frames
Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence. You should have 6 different sets of commands, one for each possible reading frame.
On a sequence_file.txt containing the sequence "agcggtatac", the command and output was as follows:
+1
cat sequence_file.txt | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[acgu]//g" SGI
+2
cat sequence_file.txt | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[acgu]//g" AVY
+3
cat sequence_file.txt | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[acgu]//g" RY
The remaining three were divided onto two lines on this wiki because they could not fit onto one without causing graphical bugs. The actual command was written without newlines.
-1
cat sequence_file.txt | sed "y/acgt/tgca/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[acgu]//g" VYR
-2
cat sequence_file.txt | sed "y/acgt/tgca/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[acgu]//g" YTA
-3
cat sequence_file.txt | sed "y/acgt/tgca/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[acgu]//g" IP
Check Your Work
Utilizing the ExPASy Translate Tool, I inputted my sample dna sequence, "agcggtatac". The result was as follows:
Links
Nicole Anguiano
BIOL 367, Fall 2015
Assignment Links
- Week 1 Assignment
- Week 2 Assignment
- Week 3 Assignment
- Week 4 Assignment
- Week 5 Assignment
- Week 6 Assignment
- Week 7 Assignment
- Week 8 Assignment
- Week 9 Assignment
- Week 10 Assignment
- Week 11 Assignment
- Week 12 Assignment
- Week 14 Assignment
- Week 15 Assignment
Individual Journals
- Individual Journal Week 2
- Individual Journal Week 3
- Individual Journal Week 4
- Individual Journal Week 5
- Individual Journal Week 6
- Individual Journal Week 7
- Individual Journal Week 8
- Individual Journal Week 9
- Individual Journal Week 10
- Individual Journal Week 11
- Individual Assessment
- Deliverables
