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. |
| 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 |
This page updated 1-28-10