ABSTRACT
In the last chapter, the focus was on nucleotide BLAST (BLASTN), a Web application that allows you to search nucleotide databases with nucleotide sequence queries. BLASTN gives you powerful search capabilities over simple text-based searches. You searched with unknowns and determined their identities based on similarities or identities to reference sequences. Now, if you were asked to find the insulin gene for the pig, you could start with the human version of insulin and search a DNA database, perhaps limiting your search to DNA sequences from Sus scrofa. There are other types of BLAST, giving you additional power and flexibility of approaches, and in this chapter we will cover protein BLAST (BLASTP, Table 4.1 ). Comparison of BLAST definition
Type
Query
Database
BLASTN
Nucleotide
Nucleotide
BLASTP
Protein
Protein
The names, BLASTN and BLASTP, are easy to remember: you use a Nucleotide query to search a nucleotide database, and a Protein query to search a protein database, respectively.