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CAP5510 Introduction to Bioinformatics
Fall 2009
Homework #2
(Assigned Sept.14. Due: Sept.21, 2009)
1.
Write in high‐level pseudo code algorithms for
(a) and (b):
(a)
Write a non‐recursive algorithm to obtain all the Fibonacci numbers of maximum size
n
.
(5 points)
(b) Given a pattern
P
of length
m
and a text
T
of length
n
over the alphabet
Σ
= (
A, C, G, T
)
for both pattern and text, compute the beginning locations of the occurrences of the
pattern
P
in
T
. (
P
may or may not occur in
T
or it might occur multiple times possibly in
overlapping fashion.) (12 points)
(c) Sketch an algorithm (“sketch” means
you explain the basic idea of the algorithm and
describe the steps in precise English language) to find the beginning locations of the
occurrences of the pattern
P
in
T
over the alphabet
Σ
= (
A, C, G, T
) such that the Hamming
distance between
P
and 
P
 consecutive characters in
T
is less than equal to 1. For example,
if
P=AGA
and
T=ATAGAGCGATA
, locations in
T
satisfying the condition are 1, 3, 5, 7, 9.
Analyze the computational complexity of your algorithm. (8 points)
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This note was uploaded on 06/12/2011 for the course CAP 5510 taught by Professor Staff during the Spring '08 term at University of Central Florida.
 Spring '08
 Staff

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