Bioinformatics and Functional Genomics, 2nd Edition

Chapter 3: Pairwise Sequence Alignment

This page offers the web documents that are referred to in Chapter 3 of the book, as well as various resources. In Chapter 3 we describe the pairwise alignment of two DNA or protein sequences. This is one of the most fundamental operations in bioinformatics. We discuss ways to assign scores to two aligned protein sequences. We also introduce ways to globally or locally align two sequences.

Web documents Pages Description
Web document 3.1 49, 51 myoglobin orthologs
Web document 3.2 49, 52 globin paralogs (13 human proteins)
Web document 3.3 56, 57 GAPDH
Web document 3.4 56 caseins
Web document 3.5 62 amino acid frequencies
Web document 3.6 80 global alignment
Web document 3.7 88 PRSS shuffle for beta globin and myoglobin
Web document 3.8 90 odorant-binding proteins


Chapter 3 Resources
Powerpoint of the pairwise alignment lecture (November 2010, Johns Hopkins School of Medicine as powerpoint)
PDF of the lecture for printing, 6 slides per page (November 2010)
Moodle site. This teaching site includes quizzes and readings; non-registered students can enter as guests
Reading assignment: Needleman & Wunsch (1970) (PMID 5420325)
Computer lab.
Globin protein sequences: human beta globin (HBB); myoglobin (MB); cytoglobin; globin from the snail Biomphalaria glabrata.
Audio file (from November 2010 here)
Key URLs: NCBI home page; align two sequences (BLAST) at NCBI; needle (global alignment) and water (local alignment) at EBI ; fasta programs at the U. Virginia; prss program at the U. Virginia; dotlet program.