BE.180:Assignment4 - Revision history

Spencers: /* Solutions */

2006-05-02T04:51:18Z

Solutions

←Older revision		Revision as of 04:51, 2 May 2006
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	**-5 for RT being incorrect, but close		**-5 for RT being incorrect, but close
	**-5 for not getting the 4 mers in listOfBestMers but getting some of them, or for finding a few too many, with the correct ones being part of the list		**-5 for not getting the 4 mers in listOfBestMers but getting some of them, or for finding a few too many, with the correct ones being part of the list
-	**-10 for being ~~way~~ off on the listOfBestMers, for example finding 1120 instead of 4, or not finding any that are correct	+	**-10 for being even further off on the listOfBestMers, for example finding 1120 instead of 4, or not finding any that are correct
	**-5 for getting bestScore wrong		**-5 for getting bestScore wrong
	**-5 total for naming variables incorrectly		**-5 total for naming variables incorrectly
	*If you have specific questions, please email Sabrina		*If you have specific questions, please email Sabrina

Spencers: /* Solutions */

2006-05-02T04:49:32Z

Solutions

←Older revision		Revision as of 04:49, 2 May 2006
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	===Solutions===		===Solutions===
	[[Media:spencers_4.txt]]		[[Media:spencers_4.txt]]
		+
		+	*The code was graded using a Protein.txt input file containing the protein "LAND" and a NC_003418.txt file containing the genome "AAAACCCCGGGGTTT".
		+	*The correct outputs are RT=YUNGCNAAYGAY, bestScore=0, listOfBestMers= ['GTTTAAAA', 'TTTTAAAA', 'GTTTTAAA', 'TTTTTAAA'].
		+	*Point breakdown: Q1: 25 points, Q2a: 10 points, Q2b: 15 points, Q2c: 25 points, Q3: 25 points
		+	*Sample point deductions:
		+	**-5 for RT being incorrect, but close
		+	**-5 for not getting the 4 mers in listOfBestMers but getting some of them, or for finding a few too many, with the correct ones being part of the list
		+	**-10 for being way off on the listOfBestMers, for example finding 1120 instead of 4, or not finding any that are correct
		+	**-5 for getting bestScore wrong
		+	**-5 total for naming variables incorrectly
		+	*If you have specific questions, please email Sabrina

Spencers: /* Solutions */

2006-04-25T22:15:40Z

Solutions

←Older revision		Revision as of 22:15, 25 April 2006
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	===Solutions===		===Solutions===
-	[[Media:spencers_4.py]]	+	[[Media:spencers_4.txt]]

Spencers: /* Corrections to problem set */

2006-04-25T22:13:23Z

Corrections to problem set

←Older revision		Revision as of 22:13, 25 April 2006
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	*From a student: "I was wondering if you could help me with the decoding rules for problem 1. I don't know if I'm interpreting them wrong, but why does it seem like the rules don't cover all possible cases? Such as for arginine, which can only be A/C in the first position, and serine, which can only be C/G in the second position. Are we supposed to assign these nucleotides with H and N respectively, even if substituting U in arginine and A/U in serine will result in a different amino acid codon?"		*From a student: "I was wondering if you could help me with the decoding rules for problem 1. I don't know if I'm interpreting them wrong, but why does it seem like the rules don't cover all possible cases? Such as for arginine, which can only be A/C in the first position, and serine, which can only be C/G in the second position. Are we supposed to assign these nucleotides with H and N respectively, even if substituting U in arginine and A/U in serine will result in a different amino acid codon?"
	**Yes, there was an oversight in the rule-making. However, please still follow the rules outlined in the pdf for the purposes of this assignment. We will not test your code with a protein containing arginine or serine.		**Yes, there was an oversight in the rule-making. However, please still follow the rules outlined in the pdf for the purposes of this assignment. We will not test your code with a protein containing arginine or serine.
		+
		+	===Solutions===
		+	[[Media:spencers_4.py]]

Spencers: /* Corrections to problem set */

2006-04-24T17:05:48Z

Corrections to problem set

←Older revision		Revision as of 17:05, 24 April 2006
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	===Corrections to problem set===		===Corrections to problem set===
	*The sentence on page one should read "If the first positions of all codons encoding an amino acid are the same, write that nucleotide’s letter to the mRNA string (i.e., A, C, U, G)", not (A, C, T, G)!		*The sentence on page one should read "If the first positions of all codons encoding an amino acid are the same, write that nucleotide’s letter to the mRNA string (i.e., A, C, U, G)", not (A, C, T, G)!
-	*From a student: "I was wondering if you could help me with the decoding rules for problem 1. I don't know if I'm interpreting them wrong, but why does it seem like the rules don't cover all possible cases? Such as for arginine, which can only	+	*From a student: "I was wondering if you could help me with the decoding rules for problem 1. I don't know if I'm interpreting them wrong, but why does it seem like the rules don't cover all possible cases? Such as for arginine, which can only be A/C in the first position, and serine, which can only be C/G in the second position. Are we supposed to assign these nucleotides with H and N respectively, even if substituting U in arginine and A/U in serine will result in a different amino acid codon?"
-	be A/C in the first position, and serine, which can only be C/G in the second position. Are we supposed to assign these nucleotides with H and N respectively, even if substituting U in arginine and A/U in serine will result in a different amino acid codon?"	+
	**Yes, there was an oversight in the rule-making. However, please still follow the rules outlined in the pdf for the purposes of this assignment. We will not test your code with a protein containing arginine or serine.		**Yes, there was an oversight in the rule-making. However, please still follow the rules outlined in the pdf for the purposes of this assignment. We will not test your code with a protein containing arginine or serine.

Spencers: /* Corrections to problem set */

2006-04-24T17:05:37Z

Corrections to problem set

←Older revision		Revision as of 17:05, 24 April 2006
Line 12:		Line 12:
	===Corrections to problem set===		===Corrections to problem set===
	*The sentence on page one should read "If the first positions of all codons encoding an amino acid are the same, write that nucleotide’s letter to the mRNA string (i.e., A, C, U, G)", not (A, C, T, G)!		*The sentence on page one should read "If the first positions of all codons encoding an amino acid are the same, write that nucleotide’s letter to the mRNA string (i.e., A, C, U, G)", not (A, C, T, G)!
-	*From a student: "I was wondering if you could help me with the decoding rules for problem 1.	+	*From a student: "I was wondering if you could help me with the decoding rules for problem 1. I don't know if I'm interpreting them wrong, but why does it seem like the rules don't cover all possible cases? Such as for arginine, which can only
-	I don't know if I'm interpreting them wrong, but why does it seem like the	+	be A/C in the first position, and serine, which can only be C/G in the second position. Are we supposed to assign these nucleotides with H and N respectively, even if substituting U in arginine and A/U in serine will result in a different amino acid codon?"
-	rules don't cover all possible cases? Such as for arginine, which can only	+
-	be A/C in the first position, and serine, which can only be C/G in the	+
-	second position. Are we supposed to assign these nucleotides with H and N	+
-	respectively, even if substituting U in arginine and A/U in serine will	+
-	result in a different amino acid codon?"	+
	**Yes, there was an oversight in the rule-making. However, please still follow the rules outlined in the pdf for the purposes of this assignment. We will not test your code with a protein containing arginine or serine.		**Yes, there was an oversight in the rule-making. However, please still follow the rules outlined in the pdf for the purposes of this assignment. We will not test your code with a protein containing arginine or serine.

Spencers: /* Corrections to problem set */

2006-04-24T17:05:08Z

Corrections to problem set

←Older revision		Revision as of 17:05, 24 April 2006
Line 12:		Line 12:
	===Corrections to problem set===		===Corrections to problem set===
	*The sentence on page one should read "If the first positions of all codons encoding an amino acid are the same, write that nucleotide’s letter to the mRNA string (i.e., A, C, U, G)", not (A, C, T, G)!		*The sentence on page one should read "If the first positions of all codons encoding an amino acid are the same, write that nucleotide’s letter to the mRNA string (i.e., A, C, U, G)", not (A, C, T, G)!
		+	*From a student: "I was wondering if you could help me with the decoding rules for problem 1.
		+	I don't know if I'm interpreting them wrong, but why does it seem like the
		+	rules don't cover all possible cases? Such as for arginine, which can only
		+	be A/C in the first position, and serine, which can only be C/G in the
		+	second position. Are we supposed to assign these nucleotides with H and N
		+	respectively, even if substituting U in arginine and A/U in serine will
		+	result in a different amino acid codon?"
		+	**Yes, there was an oversight in the rule-making. However, please still follow the rules outlined in the pdf for the purposes of this assignment. We will not test your code with a protein containing arginine or serine.

Spencers at 18:30, 17 April 2006

2006-04-17T18:30:29Z

←Older revision		Revision as of 18:30, 17 April 2006
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	Submit your one Python file to: be180hw@gmail.com. Please do not send anything other than this file to the gmail account (all questions can be sent to spencers@mit.edu or sontag@mit.edu). Please note that we will be posting the solutions to this assignment at 5pm on April 25, and we will not accept any homework after that time.		Submit your one Python file to: be180hw@gmail.com. Please do not send anything other than this file to the gmail account (all questions can be sent to spencers@mit.edu or sontag@mit.edu). Please note that we will be posting the solutions to this assignment at 5pm on April 25, and we will not accept any homework after that time.
		+
		+	===Corrections to problem set===
		+	*The sentence on page one should read "If the first positions of all codons encoding an amino acid are the same, write that nucleotide’s letter to the mRNA string (i.e., A, C, U, G)", not (A, C, T, G)!

Spencers at 18:02, 14 April 2006

2006-04-14T18:02:09Z

←Older revision		Revision as of 18:02, 14 April 2006
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	''BE.180 Homework Assignment #4 - Due on Tuesday, April 25 at 5pm''		''BE.180 Homework Assignment #4 - Due on Tuesday, April 25 at 5pm''

-	*Download Assignment 4:	+	*Download Assignment 4: [[Media:PSETfour_final.pdf]]
-	[[Media:~~Example~~.~~ogg~~]]	+
	*You will need these three input files:		*You will need these three input files:
	**Dictionary with the genetic code: [[Media:GeneticCode.dict]]		**Dictionary with the genetic code: [[Media:GeneticCode.dict]]

Spencers at 17:58, 14 April 2006

2006-04-14T17:58:19Z

←Older revision		Revision as of 17:58, 14 April 2006
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	''BE.180 Homework Assignment #4 - Due on Tuesday, April 25 at 5pm''		''BE.180 Homework Assignment #4 - Due on Tuesday, April 25 at 5pm''

-	*Download Assignment 4 [[Media:~~Pset4~~.~~pdf~~]]	+	*Download Assignment 4:
		+	[[Media:Example.ogg]]
	*You will need these three input files:		*You will need these three input files:
	**Dictionary with the genetic code: [[Media:GeneticCode.dict]]		**Dictionary with the genetic code: [[Media:GeneticCode.dict]]