Eyanosch Week 3 - Revision history

Eyanosch: create the complementary strand for the reverse -1 through -3 strands

2015-09-22T07:05:10Z

create the complementary strand for the reverse -1 through -3 strands

Eyanosch: In order to create the +2 and +3 reading frames, I took a look a the introduction to the command line and it gives these prompts to remove letters from the beginning of the command line

2015-09-22T06:53:03Z

In order to create the +2 and +3 reading frames, I took a look a the introduction to the command line and it gives these prompts to remove letters from the beginning of the command line

Eyanosch: added a space to make the coding look even

2015-09-22T06:42:58Z

added a space to make the coding look even

Eyanosch: The backbone behind the first part of the individual week 3 assignment, credit to Brandon for helping with this. He mentioned creating the three bases with a space between each other and showed me where/how to get Dondi's file

2015-09-22T06:42:26Z

The backbone behind the first part of the individual week 3 assignment, credit to Brandon for helping with this. He mentioned creating the three bases with a space between each other and showed me where/how to get Dondi's file

Eyanosch: input of the first portion of this weeks hw, using sed in a way to replace letter by letter, not whole phrases

2015-09-22T05:36:08Z

input of the first portion of this weeks hw, using sed in a way to replace letter by letter, not whole phrases

Eyanosch: added the Journal Entry Category

2015-09-21T04:19:19Z

added the Journal Entry Category

New page

[[User:Eyanosch | Erich Yanoschik]]

[[Week 3]]

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[[Category:Journal Entry]]

← Older revision		Revision as of 07:05, 22 September 2015
Line 55:		Line 55:

	*Reads for the +3 Reading Frame		*Reads for the +3 Reading Frame
		+
		+	*The Negative reading frames
		+
		+	-1 reading frame:
		+
		+	cat sequence_file \| sed "y/actg/tgac/" \| sed "s/t/u/g" \| sed "s/.../& /g" \| sed -f genetic-code.sed \| sed "s/ //g" \| sed "s/[actg]//g"
		+
		+	-2 reading frame:
		+
		+	cat sequence_file \| sed "y/actg/tgac/" \| sed "s/^.//g" \| sed "s/t/u/g" \| sed "s/.../& /g" \| sed -f genetic-code.sed \| sed "s/ //g" \| sed "s/[actg]//g"
		+
		+	-3 reading frame:
		+
		+	cat sequence_file \| sed "y/actg/tgac/" \| sed "s/^..//g" \| sed "s/t/u/g" \| sed "s/.../& /g" \| sed -f genetic-code.sed \| sed "s/ //g" \| sed "s/[actg]//g"
		+
		+
		+
		+
		+

@@ Line 43: / Line 43: @@
 * Removing all the spaces in-between the Amino Acids
-  cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed"s/[actg]//g"
+  cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed "s/[actg]//g"
 *Removes any bases accidentally left

@@ Line 43: / Line 43: @@
 * Removing all the spaces in-between the Amino Acids
-cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed"s/[actg]//g"
+ cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed"s/[actg]//g"
 *Removes any bases accidentally left

← Older revision		Revision as of 06:42, 22 September 2015
Line 18:		Line 18:
	tcgccatatg		tcgccatatg

		+	Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.
		+
		+	Using Dondi's already available translated code we first need to translate the DNA into RNA, then make a way so that the code can read each trinucleotide sequence. If it reads the entire block of code then I won't be able to use the sed commands in Dr. Dondi's page.
		+
		+
		+	cat sequence_file
		+
		+	*The file of nucleotide sequences
		+
		+	cat sequence_file \| sed "s/t/u/g"
		+
		+	*This will convert the Nucleotide sequence from DNA to RNA
		+
		+	cat sequence_file \| sed "s/t/u/g" \| sed "s/.../& /g"
		+
		+	*This command repeats every 3 nucleotides and adds a space inbetween each codon
		+
		+	cat sequence_file \| sed "s/t/u/g" \| sed "s/.../& /g" \| sed -f genetic-code.sed
		+
		+	*by taking the codes from ~dondi/xmlpipedb/data directory in a file called genetic-code.sed, 64 chain commands are already taken care of.
		+
		+	cat sequence_file \| sed "s/t/u/g" \| sed "s/.../& /g" \| sed -f genetic-code.sed \| sed "s/ //g"
		+
		+	* Removing all the spaces in-between the Amino Acids
		+
		+	cat sequence_file \| sed "s/t/u/g" \| sed "s/.../& /g" \| sed -f genetic-code.sed \| sed "s/ //g" \| sed"s/[actg]//g"
		+
		+	*Removes any bases accidentally left

← Older revision	Revision as of 05:36, 22 September 2015
Line 4:	Line 4:


	+	In order to produce the complementary strands nucleotide sequence

	+	cat sequence_file \| sed "y/atgc/tacg/"

	+	this follows the rule of y/<original characters>/<new characters>/
	+
	+	If sequence_file contains
	+
	+	agcggtatac
	+
	+	the output would be:
	+
	+	tcgccatatg