Msaeedi23 Week 3 - Revision history

Msaeedi23: invoke template

2015-09-22T04:31:44Z

invoke template

2015-09-22T04:30:19Z

‎XMLPipeDB Match Practice: match vs grep

2015-09-22T04:21:45Z

‎XMLPipeDB Match Practice: using match to determine atg pattern

2015-09-22T04:15:55Z

GO reference match utility

2015-09-22T03:53:42Z

command to account for patters

2015-09-22T03:52:21Z

frame -3

2015-09-22T03:50:59Z

frame -2

← Older revision		Revision as of 04:31, 22 September 2015
Line 84:		Line 84:
	#* 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.)
	#** Using Match searches for the three letter (ATG) and the number of times this sequence appears in the entire file. This showed that ATG appeared 830,101 times. Grep, on the other hand, counts the number of lines in which the sequence appears at least once. Meaning that ATG was found at least once on 502410 lines. The word count is the same due to the fact that there is no space between letters of a single line. Finally, there is a total amount of 35,671,048 characters in all the lines combined.		#** Using Match searches for the three letter (ATG) and the number of times this sequence appears in the entire file. This showed that ATG appeared 830,101 times. Grep, on the other hand, counts the number of lines in which the sequence appears at least once. Meaning that ATG was found at least once on 502410 lines. The word count is the same due to the fact that there is no space between letters of a single line. Finally, there is a total amount of 35,671,048 characters in all the lines combined.
		+
		+	{{Template:Msaeedi23}}

@@ Line 78: / Line 78: @@
 #** 830101 is the number of matches
 #* 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 74: / Line 74: @@
 # 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 51: / Line 51: @@
 #* <code>java -jar xmlpipedb-match-1.1.1.jar GO:000[567] < 493.P_falciparum.xml</code>
 #* 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 49: / Line 49: @@
 # 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?

@@ Line 36: / Line 36: @@
 Frame -2:
   cat "sequence_file.txt" | sed "y/acgt/tgca/" | rev | sed "s/^./ /g" | sed "s/t/u/g" | sed -f genetic-code.sed | sed "s/  / /g" | sed "s/[acgu]/ /g"
 ==== Check Your Work ====

@@ Line 33: / Line 33: @@
 Frame -1:
   cat "sequence_file.txt" | sed "y/acgt/tgca/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | sed "s/  / /g" | sed "s/[acgu]/ /g" <!-- once sequence has been reversed, use same command inputs as + frames -->
 ==== Check Your Work ====