Comp 590-087/790-087: BioAlgorithms - Fall 2011
Problem Set #2
Issued: 9/18/2011
Due: In class 10/6/2010
Homework Information: Some of the problems are probably too long to attempt the night before th
Comp 590-087/790-087: BioAlgorithms - Fall 2011
Problem Set #1
Issued: 9/4/2011
Due: In class 9/22/2010
Homework Information: Some of the problems are probably too long to attempt the night before the
4/6/16
Comp 555
Spring 2016
1
If the distance matrix D is NOT additive, then we look for a tree T
that approximates D the best:
Squared Error : i,j (dij(T) Dij)2
Squared Error is a measure of the qu
4/6/16
Comp 555
Spring 2016
1
Thus far
distance-based evolutionary trees
Additive guarantees that the tree would reproduce all
pairwise distances, but not all distance matrices are additive
Sequen
Comp 555: BioAlgorithms - Fall 2013
Problem Set #1
Issued: 9/3/2013 Due: In class 9/26/2013
SOLUTIONS
Homework Information: Some of the problems are probably too long to attempt the night before the d
The Burrows-Wheeler
Transform and
Bioinformatics
J. Matthew Holt
[email protected]
Last Class - Multiple Pattern
Matching Problem
m - length of text
d - max length of pattern
x - number of patterns
M
Programming Problem. Modify BreakpointReversalSort.py as follows:
The given version of the code outputs only one of many possible solutions. The way to generate
multiple solutions should be that if at
Chapter 7 - Pattern
Matching
J. Matthew Holt
[email protected]
Sequence Alignment
Sequencing data
Millions to billions of reads
Typically 100+ basepairs
Reference genome - millions to billions of b
9/26/13
Comp 555
Fall 2013
1
Edit Distances
Longest Common Subsequence
Global Sequence Alignment
Scoring Matrices
Local Sequence Alignment
Alignment with Affine Gap Penalties
Multiple Alignment proble
9/17/13
Comp 555
Fall 2013
1
Edit Distances
Longest Common Subsequence
Global Sequence Alignment
Scoring Matrices
Local Sequence Alignment
Alignment with Affine Gap Penalties
9/17/13
Comp 555
Fall 201
9/16/13
Comp 555
Fall 2013
1
So far weve tried: A greedy algorithm that does not
work for all inputs (it is incorrect)
New tricks weve learned
Is there an exhaustive search algorithm?
def exhaustiv
8/22/13
Comp 555
Fall 2013
1
Recall DNA is the essential
information determining the
function of living organisms
In order to understand the
biological machinery wed
like to read the code of
the gen
9/10/13
Comp 555
Fall 2013
1
An iterative algorithm where at each step
Take what seems to be the best option
Cons:
It may return incorrect results
It may require more steps than necessary
Pros:
9/11/13
Comp 555
Fall 2013
1
We developed a SimpleReversalSort algorithm that sorts
by extending its prefix on every iteration (n-1) steps.
On
: 612345
Flip 1: 1 6 2 3 4 5
Flip 2: 1 2 6 3 4 5
Flip 3
9/2/13
Comp 555
Fall 2013
1
As a precursor to transcription (the reading of
DNA to construct RNAs that eventually leading
to protein synthesis) special proteins bind to the
DNA, separate it to enable
8/29/13
Comp 555
Fall 2013
1
An algorithm is a sequence of instructions that
one must perform in order to solve a wellformulated problem.
input
Problem: Complexity
problem
algorithm
Algorithm: Correc
8/22/13
Comp 555
Fall 2013
1
Comp 555: Bioalgorithms
Suitable for undergraduate and graduate students
CS majors who want to learn bioinformatics
Non CS majors from the statistical of biological
sc
8/29/13
Comp 555
Fall 2013
1
(from Lecture 2)
Restriction enzymes break DNA whenever they
encounter specific base sequences
They occur reasonably frequently within long
sequences (a 6-base sequence