BIO/CSC 295 2011F Bioinformatics

Class 06: Gene Alignments (2)

Back to Gene Alignments (1). On to Gene Alignments (3).

This outline is also available in PDF.

Held: Tuesday, 13 September 2011

Summary: Today we explore two pattern matching algorithms: BLAST and Needleman-Wunsch. We consider the BLAST algorithm in two ways: Through an analysis of the first paper on BLAST and through experiments using an implementation of that algorithm. We visit Needleman-Wunsch by considering the design of the algorithm and by running it "by hand" on sample data.

Related Pages:

Notes:

Overview:

Having a BLAST

Our goal is to tease apart the work represented by the BLAST paper.

Some Standard Questions

Approximate Matching and Searching

The BLAST Algorithm

Exploring the Algorithm

Analyzing the BLAST Algorithm

The Needleman-Wunsch Algorithm

Dynamic Programming

Beyond Scoring

An Example of NW

Web Exploration

Back to Gene Alignments (1). On to Gene Alignments (3).

Disclaimer: I usually create these pages on the fly, which means that I rarely proofread them and they may contain bad grammar and incorrect details. It also means that I tend to update them regularly (see the history for more details). Feel free to contact me with any suggestions for changes.

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Samuel A. Rebelsky, rebelsky@grinnell.edu

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