BLAST

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Chapter 6: Anatomy of a BLAST Report

values and the gap costs) because these factors control the sensitivity and speci-

ficity of a search. The footer labels these values clearly.

Alignments

The alignments and alignment statistics reported by BLAST differ slightly from pro-

gram to program. The rest of this chapter describes the details of BLASTP, BLASTN,

BLASTX, TBLASTN, and TBLASTX alignments and shows how to recognize align-

ment groups.

BLASTP

BLASTP alignments are the simplest to understand. Figure 6-2 shows the anatomy of

a typical BLASTP alignment.

Here are the parts you should pay attention to:

Score

This value is computed from the scoring matrix and gap penalties. A higher

score indicates greater similarity. The raw score is shown without units, and the

normalized score is followed by “bits.”

Database sequence

The complete FASTA definition line is reported here along with the length of the

sequence. All the alignments between the query and a specific database sequence

are collectively called a hit. The database in Figure 6-2 has one alignment.

Figure 6-2. A BLASTP alignment

>gi|7428631|pir||GGGAA globin [validated] - slug sea hare

Length = 146

Score = 222 bits (566), Expect = 6e-58

Identities = 112/146 (76%), Positives = 127/146 (86%), Gaps = 2/146 (1%)

Query: 2 ALSAADAGLLAQSWAPVFANSAANGDSFLVALFTQFPESANFFNDFKGKSLADIQASPKL ...