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