ABSTRACT
So far, we have studied versions of BLAST which look for sequence identities and similarities within the same molecule type: BLASTN uses a nucleotide query to search a nucleotide database, and BLASTP uses a protein query to search a protein database. There are two other versions of BLAST which both cross molecular boundaries. BLASTX uses a nucleotide query to search a protein database, and TBLASTN uses a protein query to search a nucleotide database ( Table 5.1 ). BLASTX (pronounced “BLAST-ex”) and TBLASTN (pronounced “tea-BLAST-en”) are particularly useful when studying cDNA, so this chapter will begin by revisiting mRNA structure and cDNA synthesis, providing details that will make interpreting BLAST output easier. Four of the BLAST applications
Type
Query
Database
BLASTN
Nucleotide
Nucleotide
BLASTP
Protein
Protein
BLASTX
Nucleotide
Protein
TBLASTN
Protein
Nucleotide
BLASTN was covered in Chapter 3 and BLASTP was covered in Chapter 4.