Thanks to a suggestion from a reader, I ordered the O'Reilly Press book on BLAST. It just arrived and looks to be exactly what I and the rest of my lab need.
We all use BLAST all the time, but we've never really had any understanding of how our search query sequence became the search results. We sort-of knew that this was asking for trouble, but haven't taken the time to learn more. Probably this was partly because doing a BLAST search is so fast and easy that you want to use the results right away, not 'waste time' reading the manual.
The new book has a Glossary! (No more using Google to find hints of what the terms mean.) It has a detailed index! Chapter 2 has a section on Evolution, which opens with the wonderful statement that "BLAST works because evolution is happening."
Yesterday I used my newly gained ability to do local BLAST searches to set up a search for one of the post-docs. We blundered around a bit because I couldn't remember what the different letters controlling the parameter settings did. Now I have the book, all the information I need is at hand.
The only problem is that the book was published in 2002, and some details have changed. Right now I only notice that the BLAST web interface has changed a lot. The available version of BLAST has also changed, from 2.2.6 (new when the book was written) to 2.2.16. I suspect I'll need to read the book before I'll have the background to let me understand the changes.
4 hours ago in The Phytophactor