UNIT 3.11 Installing, Maintaining, and Using a Local Copy of BLAST for Intranet and Workstation Use

  1. Timothy G. Littlejohn

Published Online: 1 MAY 2004

DOI: 10.1002/0471250953.bi0311s05

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Littlejohn, T. G. 2004. Installing, Maintaining, and Using a Local Copy of BLAST for Intranet and Workstation Use. Current Protocols in Bioinformatics. 5:3.11:3.11.1–3.11.11.

Author Information

  1. IBM Life Sciences, St. Leonards, NSW, Australia

Publication History

  1. Published Online: 1 MAY 2004
  2. Published Print: MAR 2004


The Basic Local Alignment Search Tool (BLAST) is one of the widest used and most useful applications in sequence-based bioinformatics analysis. Frequently it is not practical or possible to use remote BLAST services through the Internet due to restrictions of a security or technical nature or the need for high-throughput analysis requiring greater amounts of processing power than are available from remote services. This unit describes the steps involved in obtaining and installing a copy of the BLAST software for use on a local intranet or stand-alone workstation. Once installed, the BLAST package can be used to create BLAST-searchable nucleotide and protein sequence databanks. Various popular hardware (PPC, Intel) and operating system (MacOSX, FreeBSD and Linux) options for running and maintaining the software are discussed. Finally, steps for indexing proprietary and third party (publicly available) sequence databanks for use with BLAST and managing these resources are discussed.


  • BLAST;
  • sequence similarity searching;
  • Unix-like operating systems