Relevant chapters and articles for each week

Below is a list of the relevant book chapters and articles for each course week.

 

Course Week 1 - Intro, basic molecular biology & sequence comparison

Chapter 1, page 2-5 and 60

Chapter 6, pages 330-338

 

Course Week 2 - Sequence comparison and alignment

Chapter 5, pages 224-231

 

Course Week 3 - Sequence alignment by dynamic programming

Chapter 5, pages 231-271

 

Course Week 4 - Optimal alignments in linear space + Scoring matrices

Chapter 5, pages 271-279 and 288-290

 

Course Week 5 - Heuristic database searches with protein sequences

Chapter 9, pages 510-511

 

Course Week 6 - Heuristic database searches with nucleotide sequences

BLAT article by Kent

 

Course Week 7 - Introduction to high-throughput sequencing and its applications

Chapter 3, pages 171-173

Chapter 9, page 520

 

Course Week 8 - Mapping using suffix tries, trees, and arrays, Burrows-Wheeler-transform and FM-index

Chapter 9, pages 468-528

 

Course Week 9 - Genome sequence assembly

Chapter 3, pages 116-170

Articles by Simpson & Pop and by Mathé et al.

 

Course Week 10 - Clustering

Chapter 8, pages 416-462

 

Course Week 11 - Multiple sequence alignment

Chapter 5, pages 280-285 and 293-294

 

Course Week 12 - Phylogenetic reconstruction

Chapter 7, pages 352-400

 

Course Week 13 - Motif discovery

Chapter 2, pages 66-105, 113-115

 

Course Week 14 - Searching with sequence profiles and hidden Markov models

Chapter 10, pages 530-569

HMM article by Eddy

 

Course Week 15 - Gene prediction

Chapter 11, pages 626-627

Gene prediction article by Mathé et al.

 

Published Nov. 23, 2021 1:43 PM - Last modified May 27, 2022 4:47 PM