BLAST^® Command Line Applications User Manual

This manual documents the BLAST (Basic Local Alignment Search Tool) command line applications developed at the National Center for Biotechnology Information (NCBI).

Contents

• Contributors
• Introduction
  Created: June 23, 2008; Last Update: January 7, 2021.
  • Installation
    Created: June 23, 2008; Last Update: May 16, 2024.
    • MacOSX
    • RedHat Linux
    • Source tarball
    • Building sources in Windows
    • Note regarding building the source code
  • Dependencies
    Created: June 23, 2008; Last Update: January 7, 2021.
    • Run-time
    • Compile time
  • Quick start
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Privacy
    Created: June 23, 2008; Last Update: March 24, 2022.
    • Privacy Statement
    • Opt-out of Usage Reporting
• User Manual
  Tom Madden.
  Created: June 23, 2008; Last Update: September 25, 2020.
  • Functionality offered by BLAST+ applications
    Tom Madden.
    Created: June 23, 2008; Last Update: September 25, 2020.
  • BLAST+ features
    Tom Madden and Christiam Camacho.
    Created: June 23, 2008; Last Update: March 14, 2021.
    • Tasks
    • Megablast indexed searches
    • BLAST search strategies
    • Negative GI lists
    • Masking in BLAST databases
    • Custom output formats for BLAST searches
    • Custom output formats to extract BLAST database data
    • Improved software installation packages
    • Sequence filtering applications
    • Best-Hits filtering algorithm
    • Automatic resolution of sequence identifiers
    • BLAST-WindowMasker integration in BLAST+ search applications
    • DELTA-BLAST: A tool for sensitive protein sequence search
    • Concatenation of queries
    • BLAST+ remote service
    • BLAST database metadata
    • Taxonomic filtering for BLAST databases
  • Configuring BLAST
    Tom Madden and Christiam Camacho.
    Created: June 23, 2008; Last Update: August 14, 2024.
    • Configuring BLAST via configuration file
    • Configuring BLAST via environment variables
    • Controlling concatenation of queries
    • Memory usage
    • Configure limit on the number of open files
  • Input formats to BLAST
    Tom Madden.
    Created: June 23, 2008; Last Update: September 25, 2020.
    • Multiple sequence alignment
• Cookbook
  Created: June 23, 2008; Last Update: June 30, 2023.
  • Get NCBI BLAST databases
    Created: June 23, 2008; Last Update: May 16, 2024.
  • Create a masked BLAST database
    Created: June 23, 2008; Last Update: January 7, 2021.
    • Collect mask information files
    • Create BLAST database with the masking information
    • Obtaining Sample data for this cookbook entry
  • Search with database masking enabled
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Display BLAST search results with custom output format
    Created: June 23, 2008; Last Update: January 7, 2021.
    • Example of custom output format: field selection
    • Example of custom output format: output separator
    • Trace-back operations (BTOP)
  • Use blastdb_aliastool to manage the BLAST databases
    Created: June 23, 2008; Last Update: January 7, 2021.
    • Aggregate existing BLAST databases
    • Create a subset of a BLAST database
    • Convert a GI or accession list to binary format
  • Reformat BLAST reports with blast_formatter
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Extracting data from BLAST databases with blastdbcmd
    Created: June 23, 2008; Last Update: January 7, 2021.
    • Extract lowercase masked FASTA from a BLAST database with masking information
    • Custom data extraction and formatting from a BLAST database
    • Extract different sequence ranges from the BLAST databases
    • Display the locations where BLAST will search for BLAST databases
    • Display the available BLAST databases at a given directory
  • Use Windowmasker to filter the query sequence(s) in a BLAST search
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Building a BLAST database with your (local) sequences
    Christiam Camacho.
    Created: June 23, 2008; Last Update: August 16, 2024.
  • Limiting a Search by taxonomy
    Created: June 23, 2008; Last Update: January 7, 2021.
    • Limiting a BLAST search by taxonomy
  • Limiting a Search with a List of Identifiers
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Multiple databases vs. spaces in filenames and paths
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Specifying a sequence as the multiple sequence alignment master in psiblast
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Ignoring the consensus sequence in the multiple sequence alignment in psiblast
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Performing a DELTA-BLAST search
    Created: June 23, 2008; Last Update: January 7, 2021.
    • Download the cdd_delta database
    • Execute the deltablast search
    • Indexed megaBLAST search
    • BLAST+ remote service
  • Query a BLAST database with an accession, but exclude that accession from the results
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Faster sequence lookups by accession
    Created: June 23, 2008; Last Update: January 7, 2021.
  • Threading By Query
    Tom Madden and Danae Mancinelli.
    Created: June 23, 2008; Last Update: October 31, 2023.
  • Clean-up unused database volumes
    Created: June 30, 2023; Last Update: June 30, 2023.
  • How to check BLAST database integrity?
    Created: May 16, 2024.
• Appendices
  Created: June 23, 2008; Last Update: March 14, 2021.