Do you have difficulties running high volume BLAST searches? Do you have proprietary sequence data to search and cannot use the NCBI BLAST web site? Do you have access to your own server? Do you have your own research pipeline? Have security or IP concerns about sending searches outside of your organization? If you answered yes to any of these questions, read on!
The NCBI provides a suite of command-line tools to run BLAST called BLAST+. This allows users to perform BLAST searches on their own server without size, volume and database restrictions. BLAST+ can be used with a command line so it can be integrated directly into your workflow.
What are the next steps?¶
Download and install BLAST+. Installers and source code are available from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/. Download the databases you need,(see database section below), or create your own. Start searching.
For more details, please see the BLAST+ user manual, the BLAST Help manual, the BLAST releases notes, and the article in BMC Bioinformatics (PubMed link). See our versioning policy.
The BLAST+ suite is the currently supported package. The older C toolkit executables are no longer supported. See our versioning policy.
We are always listening and welcome your feedback at BLAST Support Center.
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Read more about Magic-BLAST at NCBI Magic-BLAST Documentation
Installers and source code are available from https://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST.
IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. For details please see the documentation at https://ncbi.github.io/igblast/ and the article in Nucleic Acids Research (https://www.ncbi.nlm.nih.gov/pubmed/23671333).
Installers and source code are available from https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST.
SRPRISM is a short read alignment tool that works with genomic sequences and handles alternative loci. For more information, see https://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism/README. A LINUX executable is available under https://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism
BLAST databases are updated daily and may be downloaded via FTP from https://ftp.ncbi.nlm.nih.gov/blast/db/. Database sets may be retrieved automatically with update_blastdb.pl, which is part of the BLAST+ suite.
Please refer to the BLAST database documentation for more details.
The NCBI makes searchable collection of position-specific scoring matrices that can be used for sensitive protein and translated nucleotide searches. These are known as the Conserved Domain Database and can be searched with the RPSBLAST and RPSTBLASTN executables distributed with the BLAST+ package.
The most comprehensive collection of CDD’s is available at https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/Cdd_NCBI_LE.tar.gz.
Subsets of the comprehensive collection are available at https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/.
Documentation on these CDD collections is available at https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/README.