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Chapter 12
BLAST Search
Contents
12.1 Running BLAST searches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
12.1.1
BLAST at NCBI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
12.1.2
BLAST a partial sequence against NCBI . . . . . . . . . . . . . . . . . . 159
12.1.3
BLAST against local data . . . . . . . . . . . . . . . . . . . . . . . . . . 159
12.1.4 BLAST a partial sequence against a local database . . . . . . . . . . . . 161
12.2 Output from BLAST searches . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
12.2.1
Graphical overview for each query sequence . . . . . . . . . . . . . . . . 161
12.2.2
Overview BLAST table . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
12.2.3
BLAST graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
12.2.4
BLAST table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
12.3 Local BLAST databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
12.3.1
Make pre-formatted BLAST databases available . . . . . . . . . . . . . . 167
12.3.2
Download NCBI pre-formatted BLAST databases . . . . . . . . . . . . . . 167
12.3.3
Create local BLAST databases . . . . . . . . . . . . . . . . . . . . . . . 168
12.4 Manage BLAST databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
12.4.1
Migrating from a previous version of the Workbench . . . . . . . . . . . . 170
12.5 Bioinformatics explained: BLAST . . . . . . . . . . . . . . . . . . . . . . . . . 170
12.5.1
Examples of BLAST usage . . . . . . . . . . . . . . . . . . . . . . . . . . 171
12.5.2
Searching for homology . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
12.5.3
How does BLAST work? . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
12.5.4
Which BLAST program should I use? . . . . . . . . . . . . . . . . . . . . 173
12.5.5
Which BLAST options should I change?
12.5.6
Explanation of the BLAST output . . . . . . . . . . . . . . . . . . . . . . 175
12.5.7
I want to BLAST against my own sequence database, is this possible? . 177
12.5.8
What you cannot get out of BLAST . . . . . . . . . . . . . . . . . . . . . 178
12.5.9
Other useful resources . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
. . . . . . . . . . . . . . . . . . 174
CLC RNA Workbench offers to conduct BLAST searches on protein and DNA sequences. In short, a
BLAST search identifies homologous sequences between your input (query) query sequence and
a database of sequences [McGinnis and Madden, 2004]. BLAST (Basic Local Alignment Search
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