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.
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BLAST, like most software is always under development. Sometimes a new release adds new features (e.g. a new output option such as XML), more often it's a "maintenance release" to fix minor bugs or issues suggested by the users.
ReplyDeleteWhen you download the BLAST program from NCBI, the doc/ folder should contain a file named "history.html", which details changes between versions 2.0.4 and 2.2.10. It's also on the web. Incidentally, the NCBI FTP site is a rich source of data, programs and documentation that not many people explore in depth.
There's also a bunch of online BLAST documentation at NCBI: start here. The handbook is very good, as is the tutorial on BLAST statistics.
Books on bioinformatics and computing tend to get out of date almost as soon as they are published these days. They can be a nice introduction to a topic, but I always find online resources more useful.
Hi Neil,
ReplyDeleteFor us the big problems with learning BLAST better are (1) motivation, and (2) explanations pitched at the right level.
I knew the BLAST book would be a bit out of date, but most of what BLAST does (especially the basics) seems to have remained quite stable so I thought it would still be very relevant.
And I was pretty sure each new BLAST release would have been accompanied by a file explaining the changes, but I was also pretty sure that I wouldn't be able to understand these without first learning much more about BLAST.
I've looked at the on-line documentation; parts were helpful but many of my questions weren't addressed.
And the book was cheap! But motivation is still the big issue - I'll see how I progress.