July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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BLAST Databases
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BLAST Databases
The mechanics of creating BLAST databases is quite simple; just run formatdb or
xdformat with the proper syntax. Chapter 10 discussed this topic, and you’ll find the
command summaries in Chapters 13 and 14. There are, however, subtleties that
make this process more complicated than it may appear.
Large Databases
One of the most common database complications occurs with large files. Most com-
puters today use 32-bit operating systems and 32-bit filesystems. This puts a physi-
cal limit of 4 GB on the amount of RAM and 4 GB on the size of any particular file.
(You may find that you are actually limited to less than 4 GB in both cases, and a 2-
GB limit is quite common.) Most computers these days don’t have or need 4-GB
RAM. However, most hard disks are quite a bit larger than 4 GB, and files can some-
times exceed these limits. Therefore many operating systems have the option of using
64-bit filesystems. Unfortunately you can’t just change the filesystem and expect
everything to work. Making software applications aware of large files often means
recompiling them with special flags, and the process of migrating to a 64-bit filesys-
tem can be painful because the applications don’t tell you useful things like “I’m not
large-file-aware.” Instead, they just ...
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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.