Scientific story (html)

In brief: You're analyzing a DNA sequence you're convinced comes from a gene encoding the lethal factor of the toxinfrom Bacillus anthracis... but Blast refuses to confirm your assessment! Who's wrong and why?

Local pairwise sequence alignment
     Smith-Waterman algorithm for exact alignments
     Modified Smith-Waterman algorithm for fast, approximate alignments

Scoring schemes for sequence alignment
     Standard program to find similarities between sequences or sets of sequences.

Dissection of BlastN
     Standard program to find similarities between sequences or sets of sequences.

Perl focus: Two-dimensional arrays
Programs

Blast - NCBI implementation (various flavors you can run online at the NCBI site)

How to run BlastN (nucleotide sequence compared to nucleotide database)
How to run BlastP (protein sequence compared to protein database)
How to run Pairwise Blast (individual sequence compared to individual sequence)

BlastN - Homegrown version

We'll be using this simplified version of BlastN to investigate how BlastN works.

Consensus - Program used by notes to illustrate 2-dimensional arrays

DNA sequence alignment (PDF) (Questionnaire)
     Scoring exercises (PDF) - Scoring table problems done in class
BlastN and 2-dimensional arrays (html) (Questionnaire)
Scoring and protein alignment (PDF) (Questionnaire)
Progress on understanding BlastN (PDF) (Questionnaire)