KSherbina Week 3 - Revision history

Ksherbina: /* XMLPipeDB Match Practice */ Italicized the last mention of ATG in question 3.

2013-09-13T06:18:01Z

‎XMLPipeDB Match Practice: Italicized the last mention of ATG in question 3.

Ksherbina: /* XMLPipeDB Match Practice */ Answered the last question in the set for XMLPipeDB Match Practice.

2013-09-13T06:17:27Z

‎XMLPipeDB Match Practice: Answered the last question in the set for XMLPipeDB Match Practice.

Ksherbina: /* XMLPipeDB Match Practice */ Inputted my response to the second question.

2013-09-13T06:11:24Z

‎XMLPipeDB Match Practice: Inputted my response to the second question.

Ksherbina: Inputted response to first question in the XMLPipeDB Match Practice.

2013-09-13T06:05:22Z

Inputted response to first question in the XMLPipeDB Match Practice.

Ksherbina: /* Reading Frames */ Corrected commands to translate -1, -2, and -3 reading frames.

2013-09-13T05:56:04Z

‎Reading Frames: Corrected commands to translate -1, -2, and -3 reading frames.

Ksherbina: /* Reading Frames */ Added code to translate the -1, -2, and -3 reading frames.

2013-09-13T05:17:45Z

‎Reading Frames: Added code to translate the -1, -2, and -3 reading frames.

Ksherbina: /* Reading Frames */ Added code used to translate the +3 reading frame.

2013-09-13T02:52:24Z

‎Reading Frames: Added code used to translate the +3 reading frame.

Ksherbina: Edited a comment.

2013-09-13T00:43:53Z

Edited a comment.

Ksherbina: Entered the commands to find the amino acid sequence encoded by the +1 and +2 reading frames.

2013-09-13T00:43:14Z

Entered the commands to find the amino acid sequence encoded by the +1 and +2 reading frames.

Ksherbina: Recorded the piped text used to find the complement of a strand.

2013-09-13T00:24:29Z

Recorded the piped text used to find the complement of a strand.

@@ Line 33: / Line 33: @@
 #There are two unique matches: go:0009165 and go:0009165. The pattern go:009165 appears twice and the pattern go:009165 appears once in the file. These patterns represent a gene ontology term, which describes what biological function the product of a gene is involved in.
 #There are two unique matches: "james k.d." and "james a.a.". The pattern "james k.d." appears 8238 times while the pattern "james a.a." appears only once in the file. These patterns probably designate the names of the scientists who determined the genetic sequence of ''P. falciparum''.
-#According to Match, the pattern ''ATG'' appears 165 times in the file. However, according to ''grep'', the pattern ''ATG'' appears 162 times. The discrepancy makes sense considering that grep searches for patterns one line at a time while Match searches all of the text continuously for a specific pattern. There may have been three ATG patterns that were broken up between two consecutive lines. Thus, Match was able to find them, whereas ''grep'' was not.
+#According to Match, the pattern ''ATG'' appears 165 times in the file. However, according to ''grep'', the pattern ''ATG'' appears 162 times. The discrepancy makes sense considering that grep searches for patterns one line at a time while Match searches all of the text continuously for a specific pattern. There may have been three ''ATG'' patterns that were broken up between two consecutive lines. Thus, Match was able to find them, whereas ''grep'' was not.
 [[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:17, 12 September 2013 (PDT)

@@ Line 33: / Line 33: @@
 #There are two unique matches: go:0009165 and go:0009165. The pattern go:009165 appears twice and the pattern go:009165 appears once in the file. These patterns represent a gene ontology term, which describes what biological function the product of a gene is involved in.
 #There are two unique matches: "james k.d." and "james a.a.". The pattern "james k.d." appears 8238 times while the pattern "james a.a." appears only once in the file. These patterns probably designate the names of the scientists who determined the genetic sequence of ''P. falciparum''.
+[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:17, 12 September 2013 (PDT)
 <!--To find a pattern within text : grep "^A....T" hs_ref_GRCh37_chr19.fa-->

← Older revision		Revision as of 06:11, 13 September 2013
Line 32:		Line 32:

	#There are two unique matches: go:0009165 and go:0009165. The pattern go:009165 appears twice and the pattern go:009165 appears once in the file. These patterns represent a gene ontology term, which describes what biological function the product of a gene is involved in.		#There are two unique matches: go:0009165 and go:0009165. The pattern go:009165 appears twice and the pattern go:009165 appears once in the file. These patterns represent a gene ontology term, which describes what biological function the product of a gene is involved in.
−	#	+	#There are two unique matches: "james k.d." and "james a.a.". The pattern "james k.d." appears 8238 times while the pattern "james a.a." appears only once in the file. These patterns probably designate the names of the scientists who determined the genetic sequence of ''P. falciparum''.

← Older revision		Revision as of 06:05, 13 September 2013
Line 28:		Line 28:
	*the -1 reading frame:		*the -1 reading frame:
	cat prokaryote.txt \| sed "y/atcg/tagc/" \| rev \| sed "s/^..//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed		cat prokaryote.txt \| sed "y/atcg/tagc/" \| rev \| sed "s/^..//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed
		+
		+	===XMLPipeDB Match Practice===
		+
		+	#There are two unique matches: go:0009165 and go:0009165. The pattern go:009165 appears twice and the pattern go:009165 appears once in the file. These patterns represent a gene ontology term, which describes what biological function the product of a gene is involved in.
		+	#

@@ Line 21: / Line 21: @@
 *the -1 reading frame:
-  cat prokaryote.txt | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
+  cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
 *the -2 reading frame:
-  cat prokaryote.txt | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
+  cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
 *the -1 reading frame:
-  cat prokaryote.txt | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
+  cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed

← Older revision		Revision as of 05:17, 13 September 2013
Line 19:		Line 19:
	*the +3 reading frame:		*the +3 reading frame:
	cat prokaryote.txt \| sed "s/^..//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed		cat prokaryote.txt \| sed "s/^..//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed
		+
		+	*the -1 reading frame:
		+	cat prokaryote.txt \| rev \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed
		+
		+	*the -2 reading frame:
		+	cat prokaryote.txt \| rev \| sed "s/^.//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed
		+
		+	*the -1 reading frame:
		+	cat prokaryote.txt \| rev \| sed "s/^..//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed

← Older revision		Revision as of 02:52, 13 September 2013
Line 16:		Line 16:
	*the +2 reading frame:		*the +2 reading frame:
	cat prokaryote.txt \| sed "s/^.//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed		cat prokaryote.txt \| sed "s/^.//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed
		+
		+	*the +3 reading frame:
		+	cat prokaryote.txt \| sed "s/^..//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed

@@ Line 38: / Line 38: @@
 <!--XMLPipeDB Match Practice Task 1-->
 <!--java -jar xmlpipedb-match-1.1.1.jar "GO:000916." < 493.P_falciparum.xml-->
-:<!-- : sending a file-->
+:<!-- < : sending a file-->
 <!--There are two unique matches. First one appears twice. Second one appears once.-->

← Older revision		Revision as of 00:43, 13 September 2013
Line 7:		Line 7:
	To find the complementary strand of the sequence in the file ''prokaryote.txt'', the following sequence of piped text was executed		To find the complementary strand of the sequence in the file ''prokaryote.txt'', the following sequence of piped text was executed
	cat prokaryote.txt \| sed "y/atcg/tagc/"		cat prokaryote.txt \| sed "y/atcg/tagc/"
		+
		+	===Reading Frames===
		+
		+	The following piped sequence of text was invoked to determine the sequence of amino acids encoded by
		+	*the +1 reading frame:
		+	cat prokaryote.txt \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed
		+
		+	*the +2 reading frame:
		+	cat prokaryote.txt \| sed "s/^.//g" \| sed "s/.../& /g" \| sed "s/t/u/g" \| sed -f genetic-code.sed
		+

← Older revision		Revision as of 00:24, 13 September 2013
Line 1:		Line 1:
	{{Ksherbina}}		{{Ksherbina}}
		+
		+	==The Genetic Code, by Computer==
		+
		+	===Complement of a Strand===
		+
		+	To find the complementary strand of the sequence in the file ''prokaryote.txt'', the following sequence of piped text was executed
		+	cat prokaryote.txt \| sed "y/atcg/tagc/"
		+

	<!--To find a pattern within text : grep "^A....T" hs_ref_GRCh37_chr19.fa-->		<!--To find a pattern within text : grep "^A....T" hs_ref_GRCh37_chr19.fa-->