BLAST

This is the Title of the Book, eMatter Edition

Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.

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Chapter 8

CHAPTER 8

20 Tips to Improve

Your BLAST Searches

8.1 Don’t Use the Default Parameters

You shouldn’t use BLAST the way you use an Internet search engine such as Google.

BLAST results are very sensitive to parameters, and the defaults aren’t suitable for all

searches. Historically, BLAST parameters have changed periodically. In addition, the

NCBI-BLAST and WU-BLAST defaults have very different properties, and your

results may differ depending on where you perform your BLAST search. Thus, you

should get out of the habit of using default parameters. There are situations in which

the default parameters are just fine, but using them knowledgeably and accepting

them out of ignorance are two very different motivations. If you don’t know which

settings are appropriate for a particular search, you’re not alone; most BLAST users

don’t know how to set up a search. That’s why we wrote this book, so keep reading.

8.2 Treat BLAST Searches as Scientific

Experiments

Scientists are often taught to structure their experiments into four parts: the question

(hypothesis), the approach (experimental design), the results (data), and the interpre-

tations (beliefs). This approach shows that beliefs depend on the experiment’s data.

Whether or not an experiment is capable of answering the question is