July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 12
CHAPTER 12
Hardware and Software
Optimizations
This chapter explores how to optimize BLAST searches for maximum throughput
and will help you get the most out of your current and future hardware and soft-
ware. The first rule of BLAST performance is optimize your BLAST parameters.
Incorrect settings can cause BLAST to run slowly, and you can often achieve surpris-
ing increases in speed by adjusting a parameter or two. Chapter 9 can help you
choose the correct parameters for a particular experiment. If you’re already running
BLAST efficiently and want to get the most BLAST performance possible, read on.
The Persistence of Memory
Modern operating systems cache files. You may hear it referred to as RAM cache or
disk cache, but we’ll just call it cache. Once a file is read from the filesystem (e.g.,
hard disk), the file is kept in memory even after it is no longer used, assuming there’s
enough free RAM to do so. Why cache files? It’s frequently the case that the same file
is requested repeatedly. Retrieving from memory is much faster than from a disk, so
keeping it in memory can save a lot of time. Caching can be very important in
sequential BLAST searches if the database is located on a slow disk or across a net-
work. While the first search may be limited by the speed that
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O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.