Molecular Systematics & Evolution of Microorganisms

Table of Contents

1. Multiple Sequence Alignment
2. Alignment can be easy or difficult
3. Alignment can be guided by secondary structure
4. Homology is...
5. What is a Multiple Alignment?
6. Multiple Sequence Alignment- Goals
7. Protein Alignment can be guided by Tertiary Structure Interactions
8. Multiple Sequence Alignment- Methods
9. Manual Alignment - reasons
10. Manual Alignment- software
11. Automated Alignment - Methods
12. Dynamic programming
13. Progressive Alignment
14. Overview of the Clustal procedure
15. ClustalW- Pairwise Alignments
16. ClustalW- Guide Tree
17. ClustalW- First pair
18. ClustalW- Decision time
19. ClustalW- Alternative 1
20. ClustalW- Alternative 2
21. ClustalW- Progression
22. ClustalW-Good points/Bad points
23. ClustalW-Local Minimum
24. ClustalW- Caveats
25. ClustalW- Sequence Weighting
26. ClustalW- User-supplied values
27. ClustalW- Manipulation of penalties
28. ClustalW
29. Position-Specific gap penalties
30. Position-Specific Penalties Rule 1
31. Discouraging too many gaps 
32. Gaps in protein loops
33. Existing gaps
34. Hydrophilic residues
35. Divergent Sequences
36. Divergent Sequences- Cutoff
37. Advice on progressive alignment
38. Advice on alignments

Email: james.o.mcinerney@may.ie

Home Page: http://www.may.ie/academic/biology/jmbioinformatics.shtml