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.