Chapter 4: Basic Local Alignment Search
Tool (BLAST)
This page offers the web documents that are referred to in Chapter 4 of the book, as well as various resources. The BLAST family of programs at NCBI and elsewhere provide the most common way to search a protein or DNA sequence of interest against a database. In this chapter we discuss how to use BLAST and how it works.
| Web documents | Pages | Description |
| Web Document 4-1 | 110 |
Highly hydrophobic proteins (compositionally nonstandard) |
| Web Document 4-2 | 110 |
Cysteine-rich proteins |
| Web Document 4-3 | 110 |
AT-rich sequences (from the malaria parasite Plasmodium falciparum) |
| Web Document 4-4 | 111 |
Spectacularly repetitive DNA and protein sequences |
| Web Document 4-5 | Human beta globin (fasta format, for use in NetBlast) | |
| Web Document 4-6 | 135 |
3 proteins (used as a batch query in NetBLAST) |
Chapter 4 Resources |
| Powerpoint of the BLAST lecture (January 2008 here)(December 2008 here) |
| color pdf of the 1/08 handout; black & white PDF for printing, 6 slides per page for printing (January 2008) |
| Moodle site. This teaching site includes quizzes and readings; non-registered students can enter as guests |
| Reading assignment: paper by Altschul et al. (1990) on BLAST ( PMID: 2231712 ) |
| Computer lab (coming soon) |
| Audio file (December 2008 here) |
| Key URLs: NCBI BLAST page |
This page was updated 8-11-09