Goals

Assignment 6 Checklist

  • Use the submit command: /u/cs126/bin/submit 6 readme gene.c

  • readme
  • name, precept number
  • description of problems encountered and high level description of code
  • description of how you implemented the functions code and decode
  • use the following data instead of the one in the course packet; for each, output the position of the match, and the mapping of nucleotide triplets to amino acids (using the code supplied) for prot.2 with gene.2 and prot.3 with gene.3

  • executing
  • be sure to type a.out prot.1 gene.1 and not a.out gene.1 prot.1

  • gene.c
  • Use gene.c as starting point.
  • First get the code and decode functions working and debugged. (Hint: think in base 4. You can use integer division and remainder, or, since the base is a power of 2, right shift and bitwise AND.)
  • to aid in debugging, initialize each element of genecode[64] to '-' instead of ' '
  • the solution for the example data in gene.1 and prot.1 is gene.1.ans

    • Reference

  • the genetic data is actually cDNA (the coding region of DNA) not DNA; the mapping will be similar to RNA with t replaced by u if you wish to compare with your biology textbook (or the following table borrowed from EBB 320)
  • most of our genetic data is taken from the National Center for Biotechnology
  • here's an even larger genetic sequence containing over 67,000 nucleotides: prot.4 with gene.4