Sept. 24, 2012

Topic: BLAST and its relatives

Discussion leader:  Christina

Readings and resources:
Nucleic acid alignment
Protein alignment
NCBI Blast Introduction
NCBI Blast charts

Optional readings:
Interview with Stephen Altschul
PSI-Blast paper
Delta-Blast paper

The first two readings (From Exploring Bioinformatics by St. Clair and Visick) provide a hands-on introduction to nucleic acid and protein Blasting. For next week, work through the examples and answer the questions provided.

The next two resources are basic Blast information from the NCBI website. The charts in the second link provide an overview of the many algorithms and databases available. We'll discuss them next time.

For the students who already have plenty of experience with Blast, check out the articles on PSI-blast and Delta-Blast, as well as the interview with one of the original Blast developers, Stephen Altschul. Think about how you might explain the differences among regular Blast, PSI-Blast and Delta-Blast to the group.

PS - You might find the "Taxonomy reports" (under other reports on the blast results page) helpful when looking at bacterial taxa for questions 5&6 of the nucleotide blast project.