Bioinformatics and Functional Genomics, 2nd Edition

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 (November 2010 here)
Grayscale PDF for printing, 6 slides per page for printing (November 2010)
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)
Audiovisual file (November 2008 here)
Key URLs: NCBI BLAST page