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 February 2008 (here); December 2008 (here). |
| PDF of the handout for printing (December 2008 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 2008 here)(from December 2009 BCMB course here) |
| Key URLs: NCBI HomoloGene page; ClustalW at EBI; Pfam database |
This page updated 12-14-09