DNA (BIO/COMP 242)

Programming Assignments

(sample assignments from 2009)

• Chapter 3: Playing with Strings (Your First Perl Program)
  • String Play (zip) (now requires docs in pod; updated Aug. 12, 2009)

• Chapter 4: Regex Play
  • Regex Play
  • More with Regex (zip)

• Chapter 5: Time to do the math
  • Chargaff's Numbers (zip) (now requires docs in pod; updated Sept. 17, 2009)

• Chapter 6: Control Structures (conditionals)
  • mini Gene Finder (zip)

• Chapter 6: Control Structures (loops and regex)
  • Upstream Repeat Finder (zip)

• Chapter 7: Subroutines (modular code and more regex)
  • BLASTing seven transmembrane proteins (pdf)
  • Fuzzy Olfaction Gene Finder (zip)

• Chapter 9: Arrays and Hashes (Comparative Genomics)
  • Comparative Genomics: finding the most-frequently occurring motifs (.zip)

• Final Projects
  • Project Suggestions, Timeline, Intro-Methods Grade Key, Oral Presentation Grade Key