Chris Lewis at the U of S



Email: Christopher Lewis

857 Presentations

Links to any supplementary information related to 857 class presentations.

Presentation 1

C. Notredame, "Recent progress in multiple sequence alignment: a survey" Pharmacogenomics, Vol. 3, No. 1 (2002), pp. 131-144.

Multiple Sequence Alignments

Introduces multiple alignments: Algorithms for Multiple Sequence Alignments
Affine Gap Penalties: Affine Gap Penalties vs Regular Gap Penalties
Overview: Types of Multiple Alignment Methods
BAliBASE: BAliBASE Abstract
Glossary: NCBI - Glossary

Phylogenetics

Introduces Phylogenetics: Phylogenetics
*log: Definitions which distinguish between Homolog, Ortholog, and Paralog
Example of a simple clustering algorithm: Construction of a distance tree using clustering ... (UPGMA).
Bootstrapping: A brief "as I understand it" definition of bootstrapping
Glossaries:
EVOLUTION DISCUSSION GROUP ... : Useful terms
UCMP Glossary of Natural History Terms
Teaching Animal Molecular Phylogenetics: Glossary

Presentation 2

Haas et. al., "Primer design for large scale sequencing", Nucleic Acids Research, 1998, Vol. 26, No. 12, 3006-3012.

PCR Primer Design

Explains parameters in PCR primer design: PCR PRIMER DESIGN AND REACTION OPTIMISATION
More detailed guide to primer design: PCR and multiplex PCR: guide and troubleshooting

Suffix Trees

Information about suffix trees and other string matching algorithms: Suffix Trees
Another explanation of suffix trees: Topic #7: TRIES AND SUFFIX TREES

A Work in Progress