Chapter 3: Pairwise 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 (January 2008 here)(November 2008 here) |
| PDF of the lecture for printing, 6 slides per page (January 2008) |
| 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 2008 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. |
This page was updated 8-11-09