Anuvarsh Week 4 - Revision history

Anuvarsh: Finished part 3 of homework

2015-09-27T22:44:41Z

Finished part 3 of homework

Anuvarsh: /* What is the exact mRNA sequence that is transcribed from this gene? */ fixed some more typos

2015-09-27T22:35:41Z

‎What is the exact mRNA sequence that is transcribed from this gene?: fixed some more typos

Anuvarsh: /* What is the exact mRNA sequence that is transcribed from this gene? */ fixed a couple typos

2015-09-27T22:35:02Z

‎What is the exact mRNA sequence that is transcribed from this gene?: fixed a couple typos

Anuvarsh: finished part 2 of homework

2015-09-27T22:34:30Z

finished part 2 of homework

Anuvarsh: finished part 1 of homework

2015-09-27T21:51:56Z

finished part 1 of homework

← Older revision		Revision as of 22:44, 27 September 2015
Line 223:		Line 223:
	taccgcctgatgggcgaagagaaagaacgagtaaaaggtcggtttaaccggcctttttatt		taccgcctgatgggcgaagagaaagaacgagtaaaaggtcggtttaaccggcctttttatt

		+	==What is the amino acid sequence that is translated from this mRNA?==
		+
		+	In order to find the amino acid sequence, I can use the procedure I used before to delete everything before the start codon and everything after the stop codon. Then, I need to add spaces to separate the codons, replace all t's with u's, and use the genetic_code.sed file in order to convert the codons into their corresponding proteins. The following lines can now be deleted: 1-18, 20, 22-29 with <code>sed "1,18D;20D;22,29D"</code>. Then, I will rejoin the lines with <code>sed ':a;N;$!ba;s/\n//g'</code>. At this point, I can use the same command that I used last week in order to transcribe the mRNA sequence into it's corresponding protein sequence: <code>sed "s/t/u/g" \| sed "s/.../& /g" \| sed -f genetic-code.sed \| sed "s/ //g" \| sed "s/[aucg]//g"</code>.
		+
		+	cat infA-E.coli-K12.txt \| sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box> /1" \| sed "s/<\/minus35box>/&\n/g" \|
		+	sed "2s/[ct]at[at]at/ <minus10box>&<\/minus10box> /1" \| sed -r "s/<\/minus10box> (.){6}/&\n/g" \| sed "3s/^./
		+	<tss>&<\/tss> /g" \| sed "s/<\/tss> /&\n/g" \| sed "4s/gagg/ <rbs>&<\/rbs> /1" \| sed "s/<\/rbs> /&\n/g" \| sed "5s/atg/
		+	<start_codon>&<\/start_codon> /1" \| sed "s/<\/start_codon> /&\n/g" \| sed "6s/.../& /g" \| sed "6s/t[ag][ag]/
		+	<stop_codon>&<\/stop_codon> /1" \| sed "6s/ //g" \| sed "6s/<stop_codon>/ <stop_codon>/g" \|
		+	sed "6s/<\/stop_codon>/<\/stop_codon> /g" \| sed "s/<\/stop_codon> /&\n/g" \| sed "7s/aaaaggt/ <terminator>& \n/1" \|
		+	sed "8s/gcctttt..../&<\/terminator> /1" \| sed ':a;N;$!ba;s/\n//g' \| sed "s/ //g" \| sed "s/[<>]/\n/g" \| sed "1,18D;20D;22,29D" \|
		+	sed ':a;N;$!ba;s/\n//g' \| sed "s/t/u/g" \| sed "s/.../& /g" \| sed -f genetic-code.sed \| sed "s/ //g" \| sed "s/[aucg]//g"
		+	MAKEDNIEMQGTVLETLPNTMFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR

	{{Template:Anuvarsh}}		{{Template:Anuvarsh}}

@@ Line 208: / Line 208: @@
 - ttat
-I determined that I could delete the following lines: 1-10, 12, 14, 16, 18, 20, 22, 24, 26, 28-29. The command to these lines is <code>sed "1,10D;12D;14D;16D;18D;20D;22D;24D;26D;28,29D"</code>. After that command, I would need to rejoin all of the lines with <code>sed ':a;N;$!ba;s/\n//g'</code>. The final command that I inputted that returned just the mRNA strand was as follows:
+I determined that I could delete the following lines: 1-10, 12, 14, 16, 18, 20, 22, 24, 26, 28-29. The command to delete these lines is <code>sed "1,10D;12D;14D;16D;18D;20D;22D;24D;26D;28,29D"</code>. After that command, I would need to rejoin all of the lines with <code>sed ':a;N;$!ba;s/\n//g'</code>. The final command that I inputted that returned just the mRNA strand was as follows:
      cat infA-E.coli-K12.txt | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box> /1" | sed "s/<\/minus35box>/&\n/g" |

@@ Line 172: / Line 172: @@
 ==What is the exact mRNA sequence that is transcribed from this gene?==
-In order to find the mRNA sequence, I essentially need the sequence between the transcription start site to the terminator without the tags. I remembered the section in [[More Test Processing Features]] that talked about deleting lines, and decided to add a new line before the TSS and after the terminator, and delete the first and last line, leaving only the sequence between the TSS and terminator with it's tags. In order to delete the tags, my first thought was the make a new line before and after each tag, and delete the line that the tag sat on, and then remove all extra lines. This sounded like way too much work. Instead, I thought about the common characteristics between the tags that separates them from the DNA sequence. Obviously, DNA sequences do not have greater than or less than signs. For that reason, I decided that I could create a new line at every < or > and delete all of the lines that have a tag on them. In fact, I could create a new line on the entire tagged sequence and delete all of the lines that I don't need! After deleting all of the unnecessary lines, I just need to remove all of the line breaks using the same command as earlier. After creating the line breaks using <code>.... sed "s/ //g" | sed "s/[<>]/\n/g"</code>, I ended up with the following lines:
+In order to find the mRNA sequence, I essentially need the sequence between the transcription start site to the terminator without the tags. I remembered the section in [[More Text Processing Features]] that talked about deleting lines, and decided to add a new line before the TSS and after the terminator, and delete the first and last line, leaving only the sequence between the TSS and terminator with it's tags. In order to delete the tags, my first thought was the make a new line before and after each tag, and delete the line that the tag sat on, and then remove all extra lines. This sounded like way too much work. Instead, I thought about the common characteristics between the tags that separates them from the DNA sequence. Obviously, DNA sequences do not have greater than or less than signs. For that reason, I decided that I could create a new line at every < or > and delete all of the lines that have a tag on them. In fact, I could create a new line on the entire tagged sequence and delete all of the lines that I don't need! After deleting all of the unnecessary lines, I just need to remove all of the line breaks using the same command as earlier. After creating the line breaks using <code>... sed "s/ //g" | sed "s/[<>]/\n/g"</code>, I ended up with the following lines:
 - ttttcaccacaagaatgaatgttttcggcacatttctccccagagtgttataattgcggtcgcagagttggttacgctcattaccccgctgccgataaggaat

@@ Line 169: / Line 169: @@
      gcaaaggccgcattgtcttccgtagtcgc <stop_codon>tga</stop_codon> ttgttttaccgcctgatgggcgaagagaaagaacgagt
      <terminator>aaaaggt cggtttaaccggcctttttatt</terminator> ttat
 {{Template:Anuvarsh}}

@@ Line 128: / Line 128: @@
      ggccgcattgtcttccgtagtcgc <stop_codon>tga</stop_codon> ttgttttaccgcctgatgggcgaagagaaagaacgagtaaa
      aggtcggtttaaccggcctttttattttat
 {{Template:Anuvarsh}}