Bioinformatics and Functional Genomics, 2nd Edition

Chapter 5: Advanced Database Searching

This page offers the web documents that are referred to in Chapter 5 of the book, as well as various resources. In Chapter 4 we discussed BLAST. This chapter covers BLAST-related approaches to database searching including position-specific scoring matrices and hidden Markov models that allow far more sensitive searches. We also discuss ways to search and align long segments of genomic DNA.

Web documents Pages Description
Web Document 5-1
142
Organism-specific BLAST servers
Web Document 5-2
149
PSI-BLAST: RBP and apolipoprotein D
Web Document 5-3
154
PHI-BLAST
Web Document 5-4
158
vertebrate globins (used to make an HMM)
Web Document 5-5
158
bacterial and fungal globins (used to make an HMM)
Web Document 5-6
158
vertebrate globins: alignment for input into HMMer
Web Document 5-7
158
bacterial and fungal globins: alignment for input into HMMer
Web Document 5-8
160
hmm search (vertebrate globin query, search of human RefSeq)
Web Document 5-9
160
hmm search (bact/fungal globin query, search of human RefSeq)
Web Document 5-10
160
hmm search
Web Document 5-11
161
UCSC: basic instructions
Web Document 5-12
161
50,000 base pairs of globin DNA sequence
Web Document 5-13
161
25,000 base pairs of globin DNA sequence
Web Document 5-14
164
macaque (20,000 base pairs from globin locus)
Web Document 5-15
169
Find-a-gene project: instructions
Web Document 5-16
169
Find-a-gene example: finding a novel globin


Chapter 5 Resources
Powerpoint of the advanced BLAST lecture from February 2008 here; from June 2009 here. In 2010 we combined chapters 4 and 5 in one lecture (here).
PDF (black & white) of the handout for printing, 6 slides per page from February 2008
Moodle site. This teaching site includes quizzes and readings; non-registered students can enter as guests
Reading assignment: paper on PSI-BLAST
Key URLs: NCBI BLAST page; UCSC; Pfam database