Dynamic programming for global
alignment simple case
We want the best alignment between two sequences x and y
Consider two sequences: x1 . xM, and y1 . yM
we have ONLY three choices to get the best score F(i,j)
xi aligns to yj
Clustering expression data
What is Clustering?
Organizing data into
clusters such that there is
high intra-cluster similarity
low inter-cluster similarity
Informally, finding natural
groupings among objects.
How to score? and How to align?
Scoring, common approach: Sum of pairs or its variants for each column
S (i )
all possible pairs
Sum of pairs or SP scores
s ( xi , yi
What is phylogeny?
The inference of evolutionary relationships
The inference of putative common ancestors
Trees (with branches and leaves!)
Alignments correspond 1-to-1
with sequences of states M, X, Y
Reference: DEKM book
The circular logic
How do we know what is the right distance without
a good alignment?
And how do we construct a good alignment without
knowing what substitutions were made previously?
Genome features, and their Computational
For fourier analysis
DKEM book for HMM for bio
http:/people.cs.ubc.ca/~murphyk/Bayes/rabiner.pdf HMM theory
Computational Methods for motif detection
0204-0153.pdf (sequence logos)
Chapter-9 of DTW book for PWMs, PSSMs
Differentially Expressed Genes
Combining results from replicates
Identifying differentially expressed genes
Dealing with missing values
Static vs. time series
In many cases