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Whether you use web-BLAST or command-line BLAST tools (BLAST+), you will benefit from NCBI's transition to Accession-Based BLAST:

1. The new system uses accession-based databases that are more comprehensive than the traditional databases. They contain:

  • all records from the traditional BLAST databases — with the GeneInfo identifier (GI) removed from the record's definition line so that its accession.version is the only identifier
  • records that only have accession.version identifiers (these records were never given GI numbers and thus could not be included in traditional BLAST databases)

2. BLAST+ users will also see:

  • improved performance when limiting searches with an accession list
  • improved taxonomy-related searches/limits (taxonomy information is now bundled directly into the accession-based databases, so that lists of GIs or accessions are no longer needed)

Please access the PDF document on the BLAST+ enhancements to see detailed instructions and examples on limiting a search by taxonomy.