BLAST

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Chapter 11: BLAST Databases

sequences may not have been processed to remove sequencing vectors or low quality

reads, so the quality of the sequences varies. Finally, the htg database contains all

high-throughput genomic sequences that correspond to large genomic fragments

from various organisms.

Custom BLAST Databases

In many cases, using a custom database rather than a standard database is more effi-

cient. For example, if you’re only interested in searching against human sequences,

there’s no point in including the rest of the public database. But the total cost of a

BLAST search also includes creating the database, so it isn’t always more efficient to

use a custom database. Suppose you’ve just cloned a dog gene with mutations that

bear some similarity to a human disease, and you want to know which human pro-

teins correspond to the dog protein. You can build a human protein database and

search it, or you could search against nr and ignore anything that isn’t human. If this

is the only experiment you’re going to perform, it’s probably more efficient to search

nr than build a custom database.

If you occasionally want to make custom databases, it’s worth getting to know one of

the batch retrieval systems available on the Internet. You can make custom databases

easily using these