Kevin Wyllie Week 4 - Revision history

Kwyllie: Added my links template.

2015-09-29T06:45:06Z

Added my links template.

2015-09-29T06:44:07Z

Synax fix.

2015-09-29T06:43:26Z

Syntax edit.

2015-09-29T06:42:35Z

Finished the protocol.

2015-09-29T06:34:47Z

Added part of the protocol.

2015-09-29T06:10:57Z

Removed an unnecessary header.

← Older revision		Revision as of 06:45, 29 September 2015
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	# As done for question 2, use the appropriate modified pieces of the pipe from question 1 to find the amino acid sequence.		# As done for question 2, use the appropriate modified pieces of the pipe from question 1 to find the amino acid sequence.
−	# Once the translated sequence has been isolated, use the translation pipe from the ~~[Kevin Wyllie Week~~ 3].	+	# Once the translated sequence has been isolated, use the translation pipe from the week 3 assignment.
		+
		+
		+	===Links===
		+
		+	{{template:KwyllieJournalLinks}}

← Older revision		Revision as of 06:44, 29 September 2015
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	# As done for question 2, use the appropriate modified pieces of the pipe from question 1 to find the amino acid sequence.		# As done for question 2, use the appropriate modified pieces of the pipe from question 1 to find the amino acid sequence.
−	# Once the translated sequence has been isolated, use the translation pipe from the [~~https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Kevin_Wyllie_Week_3\| week~~ 3 ~~assignment~~].	+	# Once the translated sequence has been isolated, use the translation pipe from the [Kevin Wyllie Week 3].

← Older revision		Revision as of 06:43, 29 September 2015
Line 159:		Line 159:

	# As done for question 2, use the appropriate modified pieces of the pipe from question 1 to find the amino acid sequence.		# As done for question 2, use the appropriate modified pieces of the pipe from question 1 to find the amino acid sequence.
−	# Once the translated sequence has been isolated, use the translation pipe from [[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Kevin_Wyllie_Week_3\|week 3 assignment]].	+	# Once the translated sequence has been isolated, use the translation pipe from the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Kevin_Wyllie_Week_3\| week 3 assignment].

← Older revision		Revision as of 06:42, 29 September 2015
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	# Now just undo the line breaks.		# Now just undo the line breaks.
	#* <code> sed ':a;N;$!ba;s/\n//g' </code>		#* <code> sed ':a;N;$!ba;s/\n//g' </code>
		+
		+	====Protocol - Question 2====
		+
		+	Bits and pieces of the previous pipe can be used to find the mRNA strand.
		+
		+	# Start by beginning with the previous pipe, up until addition of the TSS tags. At this point, add the beginning tag, but not the end tag.
		+	#* <code> sed -r "s/[ct]at[at]at<\/minus10box>(.){6}/& <tss>/g" </code>
		+	# Now add the end tag (but not the beginning tag) of the terminator sequence.
		+	#* <code> sed "s/gcctttt..../&<\/terminator> /g" </code>
		+	# Then start new lines after the TSS beginning tag and before the terminator end tag.
		+	#* sed "s/<tss>/&\n/g" \| sed "s/<\/terminator>/\n&/g"
		+	# Now delete lines 1 and 3 to isolate the mRNA sequence.
		+	#* sed "3D" \| sed "1D"
		+	#* The <code> 3D </code> and <code> 1D </code> designate that lines 3 and 1 should be deleted.
		+
		+	====Protocol - Question 3====
		+
		+	# As done for question 2, use the appropriate modified pieces of the pipe from question 1 to find the amino acid sequence.
		+	# Once the translated sequence has been isolated, use the translation pipe from [[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Kevin_Wyllie_Week_3\|week 3 assignment]].

@@ Line 1: / Line 1: @@
 ==Transcription and Translation “Taken to the Next Level”==
-====Question 1====
+===Question 1===
   cat infA-E.coli-K12.txt | '''sed -r "s/tt[gt]ac[at](.){17}[ct]at[at]at/ <minus35box>&<\/minus10box> /g"'''
@@ Line 64: / Line 64: @@
-====Question 2====
+===Question 2===
 The mRNA sequence can be isolated from the file using some of the same commands as before.
@@ Line 103: / Line 103: @@
-====Question 3====
+===Question 3===
 Again, the amino acid sequence can be found by using modified bits and pieces from question 1.
@@ Line 112: / Line 112: @@
 M A K E D N I E M Q G T V L E T L P N T M F R V E L E N G H V V T A H I S G K M R K N Y I R I L T G D K V T V E L T P Y D L S K G R I V F R S R - L F Y R L M G E E K E R V K G R F N R P F Y

← Older revision		Revision as of 06:10, 29 September 2015
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	==Transcription and Translation “Taken to the Next Level”==		==Transcription and Translation “Taken to the Next Level”==
−
−	~~===Adding Tags for Each Gene "Landmark"===~~

	====Question 1====		====Question 1====