The BLAST Family of Programs



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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