- 3rd Edition home
- Resources for Teachers
- The book's webpage at Wiley
- Part I : Bioinformatics : Analyzing DNA, RNA, and Protein Sequences
- Part II: Functional Genomics: Bioinformatics from DNA to RNA to Protein
- Chapter 8: The Eukaryotic Chromosome
- Chapter 9: DNA Analysis: Microarrays and Next Generation Sequencing
- Chapter 10: Bioinformatic Approaches to RNA
- Chapter 11: RNA Analysis: Microarrays and Next Generation Sequencing
- Chapter 12: Proteomics
- Chapter 13: Protein Structure
- Chapter 14: Functional Genomics
- Part III: Genomics
- Second edition
Bioinformatics and Functional Genomics 3rd Edition
Chapter 5: Advanced BLAST
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.
- Try DELTA-BLAST, a tool that looks far deeper into protein databases than BLASTP!
- Explore HMMer software for some of the most sensitive database searches--with both web-based and command-line tools
- Learn how to search DNA queries against genomic DNA databases
- Get an introduction to the alignment of millions of next-generation sequencing reads to a large reference genome