Special Topics: Bioinformatics Computing

COSC 494/594 - Fall 2020


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
8/20/2020 DNA, genes and the genome Hw #1, due 9/1 see Piazza
8/25/2020 Sequence statistics   PDF
8/27/2020 Finalize stats; Intro to sequence alignment   PDF
9/01/2020 Sequence alignment Hw #2, due 9/15 PDF
9/03/2020 Sequence alignment heuristics   PDF
9/08/2020 Variation and natural selection   PDF
9/10/2020 Affine gap penalties; Intro to Markov Models   PDF
9/15/2020 Hidden Markov Models (Forward algorithm) Hw #3, due 9/29 PDF
9/17/2020 Hidden Markov Models (Viterbi)   PDF
9/22/2020 Gene finding using HMMs   PDF
9/24/2020 IMMs, midterm review (syncronous)   PDF
9/29/2020 Genome alignments   PDF
10/01/2020 suffix arrays, intro to genome assembly Hw #4, due 10/22
[AFG] [Reference]
10/06/2019 Online midterm    
10/08/2020 Multiple sequence alignment   PDF
10/13/2020 Genome assembly: hands on   PDF
10/15/2020 Phylogenetic analysis   PDF
10/20/2020 Phylogenetic trees: distance   PDF
10/22/2020 Other approaches for determining trees Hw #5, due 11/14
[small file] [Large file]
10/27/2020 Sequencing, Galaxy and outsourcing analysis   PDF
10/29/2020 Engineering day (no class)    
11/03/2020 Personalized medicine and human demographics    
11/05/2020 Project-linked #1: cloud and HPC for sequencing Group update #1 due  
11/10/2020 Project-linked #2: feature selection for bacterial genomics    
11/12/2020 Study hall/Projects    
11/17/2020 Project-linked #3: Data-driven mosquito control Group update #2 due  
11/19/2020 Special topic: Genomics in the news    
11/24/2020 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.