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.