Emilysimso Week 3 - Revision history

Emilysimso: Added links

2015-09-21T23:01:23Z

Added links

Emilysimso: Match section

2015-09-21T22:59:40Z

Match section

Emilysimso: Adding - reading frames

2015-09-20T17:46:01Z

Adding - reading frames

Emilysimso: Changed wording of sections

2015-09-19T03:08:14Z

Changed wording of sections

Emilysimso: Added 3 reading frames, formatting changes

2015-09-19T03:05:55Z

Added 3 reading frames, formatting changes

Emilysimso: Question 1

2015-09-19T02:45:10Z

Question 1

New page

Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.
Sequence used: gcattaggcaac
* Used sed "y/atgc/tacg/" to perform complimentary base pairing
Resulting sequence: cgtaatccgttg

← Older revision		Revision as of 23:01, 21 September 2015
Line 74:		Line 74:


		+	[[Main Page]]
	{{Template: Esimso entries etc}}		{{Template: Esimso entries etc}}

← Older revision		Revision as of 22:59, 21 September 2015
Line 41:		Line 41:
	* Used sed "s/^gu/ /g" then sed "s/ugc/C/g" sed "s/cua/L/g" sed "s/aug/M/g" then sed "s/c/ /g"		* Used sed "s/^gu/ /g" then sed "s/ugc/C/g" sed "s/cua/L/g" sed "s/aug/M/g" then sed "s/c/ /g"
	-3 Reading Frame Amino Acids: CLM		-3 Reading Frame Amino Acids: CLM
		+
		+
		+	==XMLPipeDB Match Practice==
		+	===What Match command tallies the occurrences of the pattern GO:000[567] in the 493.P_falciparum.xml file?===
		+	* Used the line: java -jar xmlpipedb-match-1.1.1.jar GO:000[567] < 493.P_falciparum.xml
		+	There are 3 unique matches
		+	go:0007 appears 113 times, go:0006 appears 1100 times, go:0005 appears 1371 times
		+
		+	===Try to find one such occurrence “in situ” within that file. Look at the neighboring content around that occurrence.===
		+	* Used grep "GO:0006" 493.P_falciparum.xml to find the lines containing the sequence
		+	* This did not give context
		+	* Used grep "...GO:0006" 493.P_falciparum.xml to find context
		+	Result: id="GO:0006506
		+	* These are ID numbers of some kinds, presumably
		+
		+	===What Match command tallies the occurrences of the pattern \"Yu.*\" in the 493.P_falciparum.xml file? ===
		+	* Used java -jar xmlpipedb-match-1.1.1.jar \"Yu.*\" < 493.P_falciparum.xml
		+	There are 3 unique matches
		+	yu b. appears 1 time, yu k. appears 228 times, yu m. also appears once
		+	* These are most likely names
		+
		+	===Use Match to count the occurrences of the pattern ATG in the hs_ref_GRCh37_chr19.fa file (this may take a while). Then, use grep and wc to do the same thing. ===
		+	* Used java -jar xmlpipedb-match-1.1.1.jar ATG < hs_ref_GRCh37_chr19.fa
		+	Total matches: 830101
		+	* This means that ATG appears together 830,101 times in the code
		+
		+	* Used grep "ATG" hs_ref_GRCh37_chr19.fa \| wc
		+	Result: 502410 502410 35671048
		+	* This means that ATG appeared in 502,410 lines and contained 35,671,048 characters
		+
		+	The two counts are different because ATG may have appeared multiple times on in a line (the 502,410), explaining why this is a lower number.
		+
		+
		+	{{Template: Esimso entries etc}}

← Older revision		Revision as of 17:46, 20 September 2015
Line 26:		Line 26:
	* Used sed "s/^gc/ /g" then sed "s/auu/I/g" then sed "s/agg/R/g" then sed "s/caa/Q/g" then sed "s/c$/ /g"		* Used sed "s/^gc/ /g" then sed "s/auu/I/g" then sed "s/agg/R/g" then sed "s/caa/Q/g" then sed "s/c$/ /g"
	+3 Reading Frame Amino Acids: IRQ		+3 Reading Frame Amino Acids: IRQ
		+
		+	===-1 Reading Frame: 5'-guu gcc uaa ugc-3'
		+	* Used see "y/t/u/" to change t's to u's from complementary strand (3'-cgtaatccgttg-5' to 3'-cguaauccguug-5')
		+	* Used echo "cguaauccguug" \| rev" to reverse the strand
		+	Resulting Stand: 5'-guugccuaaugc-3'
		+	* Used sed "s/guu/V/g" then sed "s/gcc/A/g" then "s/uaa/ stop/g" then sed "s/ugc/ /g"
		+	-1 Reading Frame Amino Acids: VA stop
		+
		+	===-2 Reading Frame: 5'-g uug ccu aau gc-3'===
		+	* Used sed "s/^g/ /g" then sed "s/uug/L/g" then "s/ccu/P/g" then "s/aau/N/g" then sed "s/gc/ /g"
		+	-2 Reading Frame Amino Acids: LPN
		+
		+	===-3 Reading Frame: 5'-gu ugc cua aug c-3'===
		+	* Used sed "s/^gu/ /g" then sed "s/ugc/C/g" sed "s/cua/L/g" sed "s/aug/M/g" then sed "s/c/ /g"
		+	-3 Reading Frame Amino Acids: CLM

@@ Line 21: / Line 21: @@
 ===+2 Reading Frame: 5'-g cau uag gca ac-3'===
 * Used sed "s/^g/ /g" then sed "s/cau/H/g" then "s/uaggcaac/ stop/g"
-  Resulting sequence: H stop
+  +2 Reading Frame Amino Acids: H stop
 ===+3 Reading Frame: 5'-gc auu agg caa c-3'===
 * Used sed "s/^gc/ /g" then sed "s/auu/I/g" then sed "s/agg/R/g" then sed "s/caa/Q/g" then sed "s/c$/ /g"
-  Resulting Sequence: IRQ
+  +3 Reading Frame Amino Acids: IRQ

@@ Line 1: / Line 1: @@
-Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.
+==Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.==
-  Sequence used: gcattaggcaac
+  Sequence used: 5'-gcattaggcaac-3'
 * Used sed "y/atgc/tacg/" to perform complimentary base pairing
-  Resulting sequence: cgtaatccgttg
+  Resulting sequence: 3'-cgtaatccgttg-5'