Nanguiano Week 3
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. For example, if sequence_file contains:
agcggtatac
Then your text processing commands for 5’-3’ frame 1 should display:
SGI
Your text processing commands for 5’-3’ frame 3 should display:
RY
...and so on.
- Hint 1: The 6 sets of commands are very similar to each other.
- Hint 2: Under the ~dondi/xmlpipedb/data directory in the Keck lab, you will find a file called genetic-code.sed. To save you some typing, this file has already been prepared with the correct sequence of sed commands for converting any base triplets into the corresponding amino acid. For example, this line in that file:
s/ugc/C/g
...corresponds to a uracil-guanine-cytosine sequence transcribing to the cysteine amino acid (C). The trick is to figure out how to use this file to your advantage, in the commands that you'll be forming.
+1
grep genetic-code.sed cat sequence_file.txt |
+2
cat sequence_file.txt | sed
+3
cat sequence_file.txt | sed
-1
cat sequence_file.txt | sed
-2
cat sequence_file.txt | sed
-3
cat sequence_file.txt | sed
Check Your Work
Fortunately, online tools are available for checking your work; we recommend the ExPASy Translate Tool, sponsored by the same people who run SwissProt. You’re free to use this tool to see if your text processing commands produce the same results.
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
