An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
The Motif Finding Problem
Given a random sample of DNA sequences:
cctgatagacgctatctggctatccacgtacgtaggtcctctgtgcgaatctatgcgtttccaaccat
agtactggtgtacatttgatacgtacgtacaccggcaacctgaaacaaacg

CIS 455 Homework #1
Due on myCourses before class on Friday, Sept. 19, 2014
Instructions: There are 6 problems worth a total of 100 points.
Submit on myCourses: solutions to the written parts, hard copies of any source code and hard copies of sample runs

CIS 455 Homework #2
Due on myCourses before class on Wednesday, October 1, 2014
Instructions: There are 6 problems worth a total of 100 points.
Submit on myCourses: solutions to the written parts, hard copies of any source code and hard copies of sample r

Introduction to
Algorithms and
Complexity
!
Chapter 2
!
f(n) is O(g(n) if there are positive real
constants c and n0 such that 0 f(n) cg(n)
for all values of n n0.
Examples:
g(n) is an asymptotic upper bound for f(n)
f(n) is (g(n) if there are positi

An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
An Introduction to Bioinformatics Algorithms
www.bi

An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
Branch and Bound Algorithm for Motif Search
Since each level of the
tree goes deeper into
search, discarding a prefix
discards all following
branches
This saves us from looking
at (n l

An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
DNA Mapping and Brute
Force Algorithms!
An Introduction to Bioinformatics Algorithms
Molecular Scissors!
www.bioalgorithms.info
An Introduction to Bioinformatics Algorithms
www.bioalgorit

An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
Finding Regulatory Motifs in
DNA Sequences
An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
Random Sample
atgaccgggatactgataccgtatttggcctaggcgtacacattagataaacgtatgaagta

An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
An Introduction to Bioinformatics Algorithms
Matlab is
installed on
the PCs in
Dion 303, and
is available on
the VCL:
w

CIS 455 Homework #3
Due on myCourses before 11:59pm on Friday, October 10th, 2014
Instructions: There are 6 problems worth a total of 100 points.
Submit on myCourses: solutions to the written parts, hard copies of any source code and hard copies of sample