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Genome Analysis: A Laboratory Manual Series Volume 1, Analyzing DNA
CHAPTER 7, Computational Analysis of DNA and Protein Sequences

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TABLE 5: The BLAST Family of Programs

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Program	Query Sequence	Database Sequences	Comments
BLASTN	Nucleotide, both strands	Nucleotide	Parameters optimized for speed, not sensitivity. Not intended for finding distantly-related coding sequences. Automatically checks for complementary strand of query. Low-complexity filter option (dust)
BLASTX	Nucleotide, six-frame translation	Protein	Very useful for preliminary data containing potential frameshift errors, i.e., ESTs and other "single-pass" sequences. 12 different genetic codes available. 65 different scoring matrices available. Low-complexity filter options with SEG or XNU algorithms (highly recommended).
TBLASTX	Nucleotide, six-frame translation	Nucleotide, six-frame translation	Very useful for preliminary data containing potential frameshift errors, i.e., ESTs and other "single-pass" sequences. 12 different genetic codes available. 65 different scoring matrices available. Low-complexity filter options with SEG or XNU algorithms (highly recommended).
BLASTP	Protein	Protein	65 different scoring matrices available. Low-complexity filter options.
TBLASTN	Protein	Nucleotide, six-frame translation	Essential for searching protein queries against EST database. Often useful for finding undocumented open reading frames or frameshift errors in database sequences. Same genetic code and scoring matrix options as BLASTX. Low-complexity filter options (highly recommended).

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