Biol 591 
Introduction to Bioinformatics
Scenarios
Fall 2002 
Alignment of mystery sequence with known anthrax toxins

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?
Bioinformatic tools
Blast
     Standard program to find similarities between sequences or sets of sequences.
Notes - Sequence alignment (PDF) (Questions)
Notes - Blast/Parsing program: 1-dimensional arrays (html); 2-dimensional arrays (html);  (Questions)
Notes - Scoring and protein alignment (PDF) (Questions)

Programs

Blast (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.
Perl focus: Arrays; Accessing characters and words within strings.

Problem Set - Just one for this scenario (PDF)