July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 12: Hardware and Software Optimizations
Software Tricks
In addition to choosing appropriate BLAST parameters and optimizing your hard-
ware set, you can use a few software tricks to increase your BLAST performance.
Most of these tricks involve splitting or concatenating sequences into optimal-sized
pieces because very large and very small sequences are inefficiently processed by
BLAST.
Multiplexing/Query Packing
Input and output (I/O) can become a large fraction of the overall CPU load when the
search parameters are insensitive, such as when running BLASTN. If you find your-
self running a lot of BLASTN searches, you can pack multiple queries together and
reduce the overhead of reading the database repeatedly. For example, let’s say you
have a collection of 100,000 ESTs from your favorite organism and you want to
search them against all other ESTs in the public database. If you search them one at a
time, you will perform 100,000 BLAST searches and therefore have to read the data-
base 100,000 times. It should go without saying that caching is essential in such a
task.
PBS The Portable Batch System (PBS) is a flexible batch queuing and workload management system originally
developed by Veridian Systems for NASA. It operates on networked, multiplatform UNIX environments, includ- ...
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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.
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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.