# Bioinformatics

Βιοτεχνολογία

2 Οκτ 2013 (πριν από 4 χρόνια και 8 μήνες)

133 εμφανίσεις

Algorithms and Pseudocode

Bioinformatics

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 d[i,j], 1<=i<=N, 1<=j<=N.

Traveling Salesman Problem

Input:

Integer N

Distances d[i,j],

1<=i<=N, 1<=j<=N

Output:

Permutation p
1

p
2

… p
N

of the

integers 1…N such that

1<=i<N
d[p
i
,p
i+1
] is the

smallest possible

String Search Problem

Input:

Strings s[1…m] and t[1…n]

Output:

The (smallest) position p

such that for all i, 1 <= i <= m,

s[i] = t[p+i
-
1];

p = 0, if no such p exists

Algorithm

String_Search(s[1…m], t[1…n])

for p = 1 to n
-
m+1 do

found = true

for i = 1 to m do

if s[i]

-
ㅝ⁴桥1

†††

if found then

break

return 0

else

return p

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