BLAST

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Chapter 11

CHAPTER 11

BLAST Databases

This chapter shows how to create and maintain BLAST databases—one of the most

neglected yet important aspects of using BLAST. We begin with a discussion of the

proper use of the FASTA format, and then turns to BLAST database issues. We fin-

ish with a general exploration of sequence databases as well as the International

Nucleotide Sequence Database.

FASTA Files

Regardless of where you get your sequences, you will eventually want them in

FASTA format because it is the standard currency for sequence data. The FASTA for-

mat has a very simple specification consisting of two parts: the definition line and the

sequence lines.

The definition line is a single line that begins with the mandatory > symbol immedi-

ately followed by an identifier and then a description. There are no spaces between

the > and the identifier. The identifier itself must not contain any whitespace

because it is the delimiter between the identifier and the description. The descrip-

tion is free-form text that may contain any characters except an end-of-line charac-

ter. Figure 11-1 shows a simple definition line in which the identifier is “EcoRI” and

the description reads “is a restriction enzyme.”

The sequence lines follow a very simple format: they may be any length and there