BNFO 602: Foundations of bioinformatics II
Spring 2017

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: TBA
Email: usman@njit.edu

Course overview: We will cover sequence alignment and phylogenetics and some genomics if time permits

Grading:

• Several short quizzes spread through the semester and one exam

Recommended texts:

• Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner
• Introduction to Bioinformatics by Arthur Lesk
• Biological Sequence Analysis by Durbin et. al.
• Algorithms on strings, trees, and sequences: computer science and computational biology by Dan Gusfield

Course plan:
   

Topic	Date	Lectures
Introduction	01/17/17	Basic bio background Python Python example 1 Python example 2 Python example 3 Pairwise sequence alignment Multiple sequence alignment Basic Unix command sheet Instructions for AFS login
Sequence alignment - Needleman-Wunsch in Python	01/24/17	Needleman Wunsch sequence alignment
Phylogenetics - maximum parsimony	01/31/17	Phylogenetics MP Tree data structure
Phylogenetics - small and big parsimony	02/07/17
Small parsimony in Python	02/14/17
Small parsimony in Python	02/21/17	Code for small parsimony Assignment 1
MP local search in Python with NNI local moves	02/28/17	Haemoglobin sequences (SWISSPROT species IDs) ClustalW webserver Haemoglobin aligned sequences Online phylogeny viewer Model tree (phylogram) Model tree (Newick text) Simulated data divergence .1 Simulated data divergence 1 Simulated data divergence 10 Simulated data divergence 100 P,L,R to newick format Code for big parsimony
NNI-based local search for MP	03/07/17	Assignment 2
Spring break	03/14/17
Phylogenetics - maximum likelihood	03/21/17	Phylogenetics ML Basic statistics Applied statistics
Phylogenetics - maximum likelihood	03/28/17
Phylogenetics - distance based methods	04/04/17	Distance based phylogenetics UPGMA implementation
Phylogenetics - UPGMA implementation	04/11/17	Assignment 3 UPGMA code
Phylogenetics - neighbor joining, bootstrapping, and MP vs. UPGMA on simulated data	04/18/17	UPGMA2 code NJ
Phylogenetics - whole genome phylogeny, bootstrapping	04/25/17	Evolutionary distances BLAST-like alignment score E.coli K12 MG1655 genome Related proteobacteria genomes Bacterial phylogeny Whole genome prokaryotic phylogeny Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices