Taur.vil Week 3 - Revision history

Taur.vil: /* Translating the Genetic Code */ correcting a typo dondi mentioned

2013-09-16T20:06:10Z

‎Translating the Genetic Code: correcting a typo dondi mentioned

2013-09-13T05:21:44Z

‎XMLPipeDB Practice: adding code

2013-09-13T05:20:44Z

‎XMLPIPEDB Practice: pipe

2013-09-13T05:03:43Z

‎Translating the Genetic Code: new category

2013-09-13T04:56:19Z

‎Translating the Genetic Code: - frames

2013-09-13T04:49:18Z

Positive Frames

2013-09-13T04:32:17Z

first creation

New page

[[Week_3|Week 3 Individual Journal]]

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[[Category: Journal Entry]]
[[Category: Individual Homework]]

@@ Line 30: / Line 30: @@
   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 Frame'''
-  cat prokaryote.txt | rev| sed "y/atcg/uagc/" | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed
+  cat prokaryote.txt | rev| sed "y/atcg/uagc/" | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed
 Produces
   - 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

@@ Line 41: / Line 41: @@
 # Match found 830,101 occurances of ATG in the code while grep/wc found 502,410. These values are different because Match counts each time the code appears while grep only counts the number of lines containing ATG (which appears multiple times in the same line).
+  grep "ATG" hs_ref_GRCh37_chr19.fa | wc
 {{Taur.vil}}

← Older revision		Revision as of 05:20, 13 September 2013
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	- 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		- 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

−	==~~XMLPIPEDB~~ Practice==	+	==XMLPipeDB Practice==
		+	# There are two unique matches: go:0009165 which appears twice and go:0009168 which appears once. I believe that the go:000916. represents an instruction that refers the web server to a particular line of code.
		+	java -jar xmlpipedb-match-1.1.1.jar "GO:000916." <493.P_falciparum.xml
		+	# Once again, there are two unique matches: james a.a. which appears once and james k.d. which appears 8,238 times. I believe the james information identifies an author.
		+	java -jar xmlpipedb-match-1.1.1.jar "James.*" <493.P_falciparum.xml
		+	# Match found 830,101 occurances of ATG in the code while grep/wc found 502,410. These values are different because Match counts each time the code appears while grep only counts the number of lines containing ATG (which appears multiple times in the same line).
		+
		+

@@ Line 33: / Line 33: @@
 Produces
   - 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
 {{Taur.vil}}

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   cat prokaryote.txt | sed "y/atcg/tagc/"
 ===Translating the Genetic Code===
-+1 Frame
+'''+1 Frame'''
   cat prokaryote.txt | sed "s/t/u/g" | sed "s/.../& /" | sed -f genetic-code.sed
 Produces
   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 Frame
+'''+2 Frame'''
   cat prokaryote.txt | sed "s/t/u/g" | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed
 Produces
   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 Frame
+'''+3 Frame'''
   cat prokaryote.txt | sed "s/t/u/g" | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed
 Produces
   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
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← Older revision		Revision as of 04:49, 13 September 2013
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	[[Week_3\|Week 3 Individual Journal]]		[[Week_3\|Week 3 Individual Journal]]

		+	==Week 2 Correction==
		+	:None were needed

		+	==Genetic Code by Computer==
		+	===Complement of a strand===
		+	cat prokaryote.txt \| sed "y/atcg/tagc/"
		+	===Translating the Genetic Code===
		+	+1 Frame
		+	cat prokaryote.txt \| sed "s/t/u/g" \| sed "s/.../& /" \| sed -f genetic-code.sed
		+	Produces
		+	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 Frame
		+	cat prokaryote.txt \| sed "s/t/u/g" \| sed "s/^.//g" \| sed "s/.../& /g" \| sed -f genetic-code.sed
		+	Produces
		+	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 Frame
		+	cat prokaryote.txt \| sed "s/t/u/g" \| sed "s/^..//g" \| sed "s/.../& /g" \| sed -f genetic-code.sed
		+	Produces
		+	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

	{{Taur.vil}}		{{Taur.vil}}