Malverso Week 3 - Revision history

Malverso: answered #4 of xmlpipedb match practice.

2015-09-22T02:00:05Z

answered #4 of xmlpipedb match practice.

2015-09-22T01:30:01Z

answered #3 for xmlpipedb match practice.

2015-09-22T01:22:47Z

answered #2 for xmlpipedb match practice.

2015-09-22T01:15:28Z

answered #1 for xmlpipedb match practice.

2015-09-22T01:05:24Z

answered reading frames for -3 strand.

2015-09-22T01:03:54Z

answered reading frames for (actual) -2 strand.

2015-09-22T01:00:40Z

answered reading frames for the (actual) -1 strand.

2015-09-22T00:54:22Z

answered reading frames for +3 strand (and fixed the signs of the first two questions)

2015-09-22T00:50:08Z

answered reading frames for -2 strand.

2015-09-22T00:45:11Z

answered Reading Frames for -1 strand.

← Older revision		Revision as of 02:00, 22 September 2015
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	From which I can infer that the information is names of people.		From which I can infer that the information is names of people.

		+	====#4====
		+	Using Match with this code:
		+	java -jar xmlpipedb-match-1.1.1.jar "ATG" < hs_ref_GRCh37_chr19.fa

		+	I found that there is 1 unique match and 830101 matches total.
		+
		+	To use grep and wc, I used the code:
		+	grep "ATG" hs_ref_GRCh37_chr19.fa \| wc
		+
		+	This showed me that there were 502410 lines, 502410 words, and 35671048 characters - which is a very different answer than what match provided. They provided different answers because grep locates the pattern on each line. since the sequence was not separated by spaces, grep interpreted each line as a word. Match, on the other hand, counts the number of pattern matches, rather than the number of lines the pattern appeared on.
		+
		+



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← Older revision		Revision as of 01:30, 22 September 2015
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	<dbReference type="GO" id="GO:0005875">		<dbReference type="GO" id="GO:0005875">

−		+	====#3====
		+	Match command:
		+	java -jar xmlpipedb-match-1.1.1.jar "\"Yu.*\"" < 493.P_falciparum.xml
		+	*There are 3 unique matches.
		+	*Matches appearances:
		+	**"yu b.": 1
		+	**"yu k.": 228
		+	**"yu m.": 1
		+	Using grep to search, I found that the appearances of the pattern were in lines such as:
		+	<person name="Yu K."/>
		+	From which I can infer that the information is names of people.
		+

@@ Line 50: / Line 50: @@
 ===XMLPipeDB Match Practice===
 I used putty.exe to access the match program, and used the [[Using the XMLPipeDB Match Utility]] page as a resource.
 Here is the Match command:
   java -jar xmlpipedb-match-1.1.1.jar "GO:000[567]" < 493.P_falciparum.xml
@@ Line 57: / Line 59: @@
 **go:0006: 1100
 **go:0005: 1371

@@ Line 7: / Line 7: @@
 ===Reading Frames===
 ====+1====
@@ Line 46: / Line 47: @@
 Which produced:
   -NAASGTGGWVIRGTWY-ATFQVQYCLLWPSYLLKYSR

← Older revision		Revision as of 01:05, 22 September 2015
Line 40:		Line 40:
	This was the result:		This was the result:
	LKCRQRNWRLGYTRNMVLGNVSSSILSSLAIVPIEI--		LKCRQRNWRLGYTRNMVLGNVSSSILSSLAIVPIEI--
		+
		+	====-3====
		+	And finally, I took off two characters from the beginning of the line instead of one:
		+	cat prokaryote.txt \| rev prokaryote.txt \| sed "s/^..//g" \| sed "y/agtc/tcag/" \| sed "s/.../& /g" \| sed "y/t/u/" \| sed -f genetic-code.sed \| sed "s/[aguc]//g" \| sed "s/ //g"
		+	Which produced:
		+	-NAASGTGGWVIRGTWY-ATFQVQYCLLWPSYLLKYSR
		+

@@ Line 34: / Line 34: @@
 which produced:
   VKMPPAELAAGLYAEHGIRQRFKFNIVFFGHRTY-NIV
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@@ Line 13: / Line 13: @@
 I tried cat prokaryote.txt | sed “y/t/u/” | sed –f genetic-code.sed, but when I checked that answer on the ExPASy Translate Tool  it was wrong. Then I tried adding a space between each set of three letters with sed “s/…/& /g” which produced the correct answer but with some left over bases on the end.I added sed “s/[augc]//” to get rid of the left over bases, and then sed "s/ //g" to get rid of the spaces between the letters.
 This looked like:
-  cat prokaryote.txt | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[atgc]//g" | sed "s/ //g"
+  cat prokaryote.txt | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[augc]//g" | sed "s/ //g"
 which had the output:
   STIFQ-VRWPKKTILNLKRCLIPCSAYNPAASSAGGIL
@@ Line 28: / Line 28: @@
 which proved to be successful:
   YYISIGTMAKEDNIELETLPNTMFRV-PSRQFRWRHFN
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@@ Line 8: / Line 8: @@
 ===Reading Frames===
-====-1====
+====+1====
 Using prokaryote.txt again, I used sed “y/t/u/” to replace all the t's with u's. I then re-read [[Introduction to the Command Line]] to find that sed –f <file with rules> is the technique I should use to use to harness the helpfullness of the genetic_code.sed file.
@@ Line 17: / Line 17: @@
   STIFQ-VRWPKKTILNLKRCLIPCSAYNPAASSAGGIL
-====-2====
+====+2====
 For this strand, the only change I had to make in my code was to get rid of the very first character of prokaryote.txt. At first, I added the command sed "s/^[agtc]//g", but realized that it also worked to use sed "s/^.//g". I chose the second choice which looked like:
   cat prokaryote.txt | sed "s/^.//g" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[augc]//g" | sed "s/ //g"
@@ Line 23: / Line 23: @@
   LLYFNRYDGQRRQY-T-NVA-YHVPRITQPPVPLAAF-
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← Older revision		Revision as of 00:45, 22 September 2015
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	cat prokaryote.txt \| sed "y/atgc/tacg/"		cat prokaryote.txt \| sed "y/atgc/tacg/"

		+	===Reading Frames===
		+
		+	====-1====
		+	Using prokaryote.txt again, I used sed “y/t/u/” to replace all the t's with u's. I then re-read [[Introduction to the Command Line]] to find that sed –f <file with rules> is the technique I should use to use to harness the helpfullness of the genetic_code.sed file.
		+
		+	I tried cat prokaryote.txt \| sed “y/t/u/” \| sed –f genetic-code.sed, but when I checked that answer on the ExPASy Translate Tool it was wrong. Then I tried adding a space between each set of three letters with sed “s/…/& /g” which produced the correct answer but with some left over bases on the end.I added sed “s/[augc]//” to get rid of the left over bases, and then sed "s/ //g" to get rid of the spaces between the letters.
		+	This looked like:
		+	cat prokaryote.txt \| sed "s/.../& /g" \| sed "y/t/u/" \| sed -f genetic-code.sed \| sed "s/[atgc]//g" \| sed "s/ //g"
		+	which had the output:
		+	STIFQ-VRWPKKTILNLKRCLIPCSAYNPAASSAGGIL


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