Difference between revisions of "Nanguiano Week 3"

Revision as of 21:40, 15 September 2015

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 because they could not fit onto one.

-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 | sedsed "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 | sedsed "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

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

Shared Journals

• Class Journal Week 1
• Class Journal Week 2
• Class Journal Week 3
• Class Journal Week 4
• Class Journal Week 5
• Class Journal Week 6
• Class Journal Week 7
• Class Journal Week 8
• Class Journal Week 9
• Class Journal Week 10
• Class Journal Week 11
• Class Journal Week 12
• Class Journal Week 14
• Class Journal Week 15