Algorithms and Pseudocode

1
Algorithms and Pseudocode

• Bioinformatics

2
Formulating Problems

• Clarify input and output elements
• Requires modeling the problem in some concise
  form
• Example Given n cities and distances between
  cities, find the shortest tour
• More concise description of input integer N,
  distances di,j, 1ltiltN, 1ltjltN. What about
  output?

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Traveling Salesman Problem

• Input Integer N Distances di,j, 1ltiltN,
  1ltjltN
• Output Permutation p1 p2 pN of the integers
  1N such that ?1ltiltN dpi,pi1 is
  the smallest possible

4
String Search Problem

• Input Strings s1m and t1n
• Output The (smallest) position p such that for
  all i, 1 lt i lt m, si tpi-1 p 0,
  if no such p exists

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Algorithm

• String_Search(s1m, t1n)
• for p 1 to n-m1 do
• found true
• for i 1 to m do
• if si ? tpi-1 then
• found false
• if found then
• break
• if not found then
• return 0
• else
• return p

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Algorithm Specification

• Pseudocode not tied to a particular programming
  language syntax
• Data
• Variables
• Arrays
• Statements
• Assignments and computation
• Decisions, conditions, and loops
• Break and return