Special Topics: Bioinformatics Computing

COSC 494/594 - Fall 2018


Scott Emrich
Office: 608 Min Kao
Phone: (865) 974-3891; E-mail: semrich at utk.edu
Office hours: Mondays, 4-5pm and by appointment


Broad overview of bioinformatics with a substantial problem-solving component. Topics include: generative models for sequences, pairwise sequence alignment, basic methods in molecular phylogeny and evolution, ab initio gene prediction, whole genome comparisons, genome assembly and analysis.

Text and syllabus

Introduction to Computational Genomics by Cristianini and Hahn.

The syllabus can be found here

Draft schedule

Date Topic Homework Notes
8/23/2018 DNA, genes and the genome Hw #1 out, due 9/3 see Piazza
8/28/2018 Sequence statistics   PDF
8/30/2018 Finalize stats; Intro to sequence alignment   PDF
9/04/2018 Sequence alignment Hw #2 out, due 9/18 PDF
9/06/2018 Sequence alignment heuristics   PDF
9/11/2018 Variation and natural selection   PDF
9/13/2018 Affine gap penalties; Intro to Markov Models   PDF
9/18/2018 Hidden Markov Models (Forward algorithm) Hw #3 out, due 10/2 PDF
9/20/2018 Hidden Markov Models (Viterbi)   PDF
9/25/2018 Gene finding using IMMs and HMMs   PDF
9/27/2018 Special topic: Bioinformatics and Plant tech (at Calhoun's)    
10/02/2018 Midterm review, suffix trees and suffix arrays   PDF
Fall break!
10/9/2018 In-class midterm    
10/11/2018 Suffix arrays Hw #4 out, due 10/30
[AFG for asm][reference]
See Piazza
10/16/2018 Finish genome alignment   PDF
10/18/2018 Genome assembly   PDF
10/23/2018 Genome assembly: hands on   PDF
10/25/2018 Engineering day    
10/30/2018 Phylogenetic analysis   PDF
11/01/2018 Phylogenetic trees: distance Hw #5 out, due 11/15
[small FASTA] [Large Phylip file]
11/06/2018 Other approaches for determining trees, intro to metagenomics   PDF
11/08/2018 Multiple sequence alignent Group update #1 due PDF
11/13/2018 Sequencing, Galaxy and outsourcing analysis   PDF
11/15/2018 Personalized medicine and human demographics    
11/20/2018 Project-linked #1: cloud and HPC for sequencing    
11/27/2018 Project-linked #2: randomized algs (LSH, minhash) Group update #2 due  
11/29/2018 Special topic: Genomics in the news    
12/04/2018 Project presentations    

Academic dishonesty

All are required to abide by the University honor code. Discussions are encouraged, but all answers/programs must be written/developed individually.

Final projects will be performed as a group with peer assessments.