Difference between revisions of "Kmeilak Week 3"

Latest revision as of 05:50, 13 September 2013

[edit] Week 2 (corrected)

Kmeilak Week 2

[edit] Where's your stuff?

Was unable to successfully upload .txt or .html files. However, I was able to successfully make an html file that was opened by a web browser and is saved on my computer at this location [file:///C:/Users/Kevin/Desktop/Week%203%20homework.html link to Kevin's html]

[edit] The Genetic Code by Computer

[edit] Complement of a Strand

The way to return a strand's complement is by inputting the following

cat prokaryote.txt | sed "y/atcg/tagc/"

[edit] Reading Frames

• +1 strand:

cat prokaryote.txt | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed

translates as

S T I F Q - V R W P K K T I L N L K R C L I P C S A Y N P A A S S A G G I L

• +2 strand:

cat prokaryote.txt | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed

translates as

L L Y F N R Y D G Q R R Q Y - T - N V A - Y H V P R I T Q P P V P L A A F -

• +3 strand:

cat prokaryote.txt | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed

translates as

Y Y I S I G T M A K E D N I E L E T L P N T M F R V - P S R Q F R W R H F N

• -1 strand:

cat prokaryote.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed

translates as

V K M P P A E L A A G L Y A E H G I R Q R F K F N I V F F G H R T Y - N I V

• -2 strand:

cat prokaryote.txt | sed "y/atcg/uagc/" | sed "s^.//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed

translates as

L K C R Q R N W R L G Y T R N M V L G N V S S S I L S S L A I V P I E I - -

• -3 strand:

cat prokaryote.txt | sed "y/atcg/uagc/" | sed "s^..//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed

translates as

- N A A S G T G G W V I R G T W Y - A T F Q V Q Y C L L W P S Y L L K Y S R

[edit] XMLPipeDB Match Practice

1. The Match command that tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file sends the web server to a line of code.

• There are 2 unique matches
• the first unique match (go:0009165) appears twice, and the second unique match (go:0009168) appears once
• The pattern GO:000916. represents

2. The Match command that tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file is an author.

• There are 2 unique matches
• The first unique match ("james k.d.") appears 8238 times and the second unique match ("james a.a.") appears 1 time
• The pattern \"James.*\" represents

3. ATG Results

• The answer Match gave me was that ATG appeared 830101 times
• grep/wc said that ATG appeared 502410 times
• Yes, these responses do make sense. Match looks only for the pattern ATG, but grep/wc searches for the number of lines of code where the sequence appears, which means any lines with multiple appearances of ATG are counted as a single result.

• Main Page
• Kevin's User Page
• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 13
• Week 14
• Week 15
• 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 13
• Class Journal Week 14
• Class Journal Week 15
• Kmeilak Week 2
• Kmeilak Week 3
• Kmeilak Week 4
• Kmeilak Week 5
• Kmeilak Week 6
• Kmeilak Week 7
• Kmeilak Week 8
• Kmeilak Week 9
• Kmeilak Week 10
• Kmeilak Week 11
• Kmeilak Week 12
• Kmeilak Week 13
• Kmeilak Week 14
• Kmeilak Week 15

Kmeilak (talk) 21:20, 12 September 2013 (PDT)