BE.180:Assignment4: Difference between revisions
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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. | *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. | ||
Revision as of 10:05, 24 April 2006
BE.180 Homework Assignment #4 - Due on Tuesday, April 25 at 5pm
- Download Assignment 4: Media:PSETfour_final.pdf
- You will need these three input files:
- Dictionary with the genetic code: Media:GeneticCode.dict
- Text file with protein sequence: Media:Protein.txt
- Text file with genome: Media:NC_003418.txt
- When saving these files, make sure the file names are uppercase.
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)!
- 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.
