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NCBI is transitioning to Accession-Based BLAST in stages. As of January 2019, we have converted some* of the most popular traditional (GI-based) BLAST databases into accession-based format.  If you are a BLAST+ (command-line tools) user and you want to benefit from the new system, you will need to (1) access Accession-Based BLAST databases and (2) use BLAST+ version 2.8.0 or newer:

1. You can access the Accession-Based BLAST databases in two ways:

2. Use the link to the latest version BLAST+ executables (the latest version in January 2019 is 2.8.1; see the release notes). 

For general guidelines on using BLAST+ command line tools, refer to the BLAST® Command Line Applications User Manual. Check the PDF document for specific enhancements that we introduced with the Accession-Based BLAST, including new ways of limiting searches by taxonomy. 

*Please let us know (write to blast-help@ncbi.nlm.nih.gov ) if you need a specific BLAST database and we will do our best to provide it for you.