Homework 1 (due 2/7/05)
1. Find the optimal alignment of the following two sequences:
AGGCTATCACCTGACCTCCAGGCCGATGCCC
TAGCTATCACGACCGCGGTCGATTTGCCCGAC
The scoring functions are: match=1, mis-match=-1, and indel=-1.
You are asked to complete the alignment

10-810 Advanced Algorithms and Models for
Computational Biology: a machine learning approach.
Problem Set 3
This problem set is due on Monday, 03/27 in class.
Cubic splines
We have discussed the use of cubic splines to represent time series expression dat

10-810, Computational Molecular Biology: a machine
learning approach: Problem Set 2
This problem set is due on Monday, 03/06 in class.
Bipartite graphs and whole genome alignment
Given genomes from two species, A and B we discussed in class a bipartite gr

Homework 4: due 4/19
Molecular Evolution:
1. Why the empirical percentage of sequence difference between species needs to be
rescaled when used as evolutionary distance?
2. For the Jukes-Cantor and Kimura models, the uniform distribution is stationary. Is