Harvard:Biophysics 101/2007/03/15

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?