5.1 The Five BLAST Programs

The five traditional BLAST programs are: BLASTN, BLASTP, BLASTX, TBLASTN, and TBLASTX. BLASTN compares nucleotide sequences to one another (hence the N). All other programs compare protein sequences (see Table 5-1).

Table 5-1. Traditional BLAST programs

Program	Database	Query	Typical uses
BLASTN	Nucleotide	Nucleotide	Mapping oligonucleotides, cDNAs, and PCR products to a genome; screening repetitive elements; cross-species sequence exploration; annotating genomic DNA; clustering sequencing reads; vector clipping
BLASTP	Protein	Protein	Identifying common regions between proteins; collecting related proteins for phylogenetic analyses
BLASTX	Protein	Nucleotide translated into protein	Finding protein-coding genes in genomic DNA; determining if a cDNA corresponds to a known protein
TBLASTN	Nucleotide translated into protein	Protein	Identifying transcripts, potentially from multiple organisms, similar to a given protein; mapping a protein to genomic DNA
TBLASTX	Nucleotide translated into protein	Nucleotide translated into protein	Cross-species gene prediction at the genome or transcript level; searching for genes missed by traditional methods or not yet in protein databases

You'll also find several BLAST derivatives and BLAST wrappers (scripts that run BLAST in a specialized way) with names such as PSI-BLAST, PHI-BLAST, MegaBLAST, BLASTZ, XBLAST, MPBLAST, HT-BLAST, and GENE-BLAST. This book—and especially this chapter—deals primarily with the five traditional programs. If you are familiar with the details of these algorithms, you will have a solid foundation for understanding the variants.