Bioinformatics and Functional Genomics, 2nd Edition

Chapter 6: Multiple Sequence Alignment

This page offers the web documents that are referred to in Chapter 6. In Chapter 3 we discussed pairwise alignment, and then in Chapters 4 and 5 we described how a protein or DNA query can be compared to a database. This chapter covers a series of approaches to multiple sequence alignment, including the popular method of progressive alignment and new methods such as consistency-based and structure-based alignment. We also discuss ways to multiply align long segments of genomic DNA.

Web documents

Pages

Description
Web Document 6-1
183
HOMSTRAD database globins
Web Document 6-2
183
HOMSTRAD database lipocalins
Web Document 6-3
184, 208
Set of distantly related globins
Web Document 6-4
184, 208
Set of closely related globins
Web Document 6-5
194
Output of M-Coffee alignment of distantly related globins
Web Document 6-6
196
Output of iRMSD-APDB for divergent globins
Web Document 6-7
196
Output of iRMSD-APDB for closely related globins
Web Document 6-8
207
Links to multiple sequence alignment programs
Web Document 6-9
208
Set of distantly related lipocalins


Chapter 6 Resources
Powerpoint of the multiple sequence alignment lecture from December 2010 (here).
Grayscale PDF of the handout for printing (December 2010 here)
Moodle site. This teaching site includes quizzes and readings; non-registered students can enter as guests
Reading assignment: paper on ClustalW (1994)
Audio file from December 2009 BCMB course (here)
Key URLs: NCBI HomoloGene page; ClustalW at EBI; Pfam database