Harvard:Biophysics 101/2007/03/15

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Assignment Due Mar 20

Overview

  • It may be too difficult for everyone to parse the entire set of examples by Tuesday.
  • Instead, we will split into groups for a divide & conquer strategy.
  • Each group only needs to produce one script. All group members should post their group's solution to individual notebook pages.
  • Please provide rich and detailed documentation. Try to match the source code style of the BioPython package (including docstrings).
  • Your script(s) should be able to properly parse the following:
    • Input file 1 (March 13 exercise)
    • A subset of input file 2: all mystery sequences contributed by the members of that group.
    • Input file 3 (March 15 teaching staff contribution)

Group Assignments

  • Kay Aull ↔ Tiffany Chan
  • Resmi Charalel ↔ Cynthia Chi
  • Katie Fifer ↔ Hetmann Hsieh
  • Deniz Kural ↔ Christopher Nabel
  • Zachary Sun ↔ Michael Wang ↔ Xiaodi Wu

Input files

  • File 1: smd.fasta
    • This file contains the sequence from the March 13 assigned for "manual" completion.
  • File 2: class.fasta
    • This file contains all student sequences.
  • File 3: ms.fasta
    • This file contains two sequences.
    • The first is an exonic sequence of a gene. Which gene is it? Is it mutated? Is the allele implicated in disease? Which diseases?
    • The second is a sequence of a gene. Which gene is it? Is it mutated? Is the allele implicated in disease? Which diseases?
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