Computational Molecular Biology, aka Algorithms for Computational Biology Home * Syllabus * Course Information * Lecturers,TAs, office hours * Forum

Alignment Module Guide

Wednesday, October 7

• Intro to Needleman-Wunsch and Smith-Waterman (Also see Alignment Notes)
• Alignment Assignment 1

Friday, October 9

• Intro to Pair HMMs (Also see Alignment Notes)
• Workshop alignment programming assignment

Monday, October 12

• Introduction to short reads (Short read notes #1)

• Read this primer on aligning short reads to genomes

Wednesday, October 14

• More on posterior confidence of read placement (Short read notes #1)
• Aligning short reads (Short read notes #2)
• Here is a paper with more details for those interested

Friday October 16

• **No class: Fall Break**

Monday October 19

• More on aligning short reads (Short read notes #2)
• Suffix arrays, suffix trees, and Burrows-Wheeler transform applied to short read alignment (Short read notes #3)
• Here is a paper with more details on BWA for those interested

• Short read alignment programming assignment. You can unpack the assignment by running the following command on warlord: 'tar xvjf 587-alignment-homework.bz2'

Wednesday October 21

• Multiple sequence alignment