Anuvarsh Week 3 - Revision history

Anuvarsh: Added template

2015-09-20T08:40:29Z

Added template

Anuvarsh: Finished the match practice

2015-09-20T08:06:37Z

Finished the match practice

Anuvarsh: /* Check Your Work */ added details and fixed formatting

2015-09-20T07:30:31Z

‎Check Your Work: added details and fixed formatting

← Older revision		Revision as of 08:40, 20 September 2015
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	#* Explain why the counts are different. (''Hint:'' Make sure you understand what exactly is being counted by each approach.)		#* Explain why the counts are different. (''Hint:'' Make sure you understand what exactly is being counted by each approach.)
	#** Match provides a statistic that represents the total number of times the search parameter was found within the file. Within hs_ref_GRCh37_chr19.fa, "ATG" appears 830,101 times. Grep looks for the search parameter in every line of a specific file and returns a list that consolidates every line that has an instance of that search parameter. Wc provides 3 statistics representing line count, word count, and character count respectively. Within hs_ref_GRCh37_chr19.fa, grep found 502,410 lines that contain "ATG". Because there are no spaces in genetic code, each line was considered a word, so wc reported that there are 502,410 words, and a total of 35,671,048 characters accumulated through each of those lines/words.		#** Match provides a statistic that represents the total number of times the search parameter was found within the file. Within hs_ref_GRCh37_chr19.fa, "ATG" appears 830,101 times. Grep looks for the search parameter in every line of a specific file and returns a list that consolidates every line that has an instance of that search parameter. Wc provides 3 statistics representing line count, word count, and character count respectively. Within hs_ref_GRCh37_chr19.fa, grep found 502,410 lines that contain "ATG". Because there are no spaces in genetic code, each line was considered a word, so wc reported that there are 502,410 words, and a total of 35,671,048 characters accumulated through each of those lines/words.
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		+	{{Template: Anuvarsh}}

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      cp prokaryote.txt ~avarshne/biodb2015
      cp infA-E.coli-K12.txt ~avarshne/biodb2015
+    cp 493.P_falciparum.xml ~avarshne/biodb2015
@@ Line 121: / Line 122: @@
 # What Match command tallies the occurrences of the pattern <code>GO:000[567]</code> in the ''493.P_falciparum.xml'' file?
 #* How many unique matches are there?
 #* How many times does each unique match appear?
 # Try to find one such occurrence “in situ” within that file. Look at the neighboring content around that occurrence.
 #* Describe how you did this.
 #* Based on where you find this occurrence, what kind of information does this pattern represent?
 # What Match command tallies the occurrences of the pattern <code>\"Yu.*\"</code> in the ''493.P_falciparum.xml'' file?
 #* How many unique matches are there?
 #* How many times does each unique match appear?
 #* What information do you think this pattern represents?
 # Use Match to count the occurrences of the pattern <code>ATG</code> in the ''hs_ref_GRCh37_chr19.fa'' file (this may take a while).  Then, use '''grep''' and '''wc''' to do the same thing.
 #* What answer does Match give you?
 #* What answer does '''grep''' + '''wc''' give you?
 #* Explain why the counts are different. (''Hint:'' Make sure you understand what exactly is being counted by each approach.)

@@ Line 107: / Line 107: @@
 == Check Your Work ==
-I checked my work with ExPASy Translate Tool.
+I checked my work with ExPASy Translate Tool. I input my original DNA strand (agcgguauac), and received the following results from the translator:
 * 5'3' Frame 1: S G I
@@ Line 116: / Line 116: @@
 * 3'5' Frame 3: I P
-=== XMLPipeDB Match Practice ===
+== XMLPipeDB Match Practice ==
 For your convenience, the XMLPipeDB Match Utility (''xmlpipedb-match-1.1.1.jar'') has been installed in the ''~dondi/xmlpipedb/data'' directory alongside the other practice files. Use this utility to answer the following questions: