BLAST stands for 'Basic Local Alignment Search Tool', which was first described by Altschul et al in 1990 [1]. It was further enhanced to perform gapped local alignment (version 2.0) in 1997 [2]. Using the BLAST engine, NCBI has been providing sequence alignment services since 1991, initially through an email server (decommissioned in 2001) and later through its web server (since 1995).
The URLAPI is a protocol for end users to interact with a web service using the commands encoded within a URL. The BLAST URLAPI from NCBI, previously known as QBlAst, allows users to submit BLAST search requests using URL encoded commands and parameters. The current server is powered by a distributive computing system called splitd (split database). A poster presentation describing the setup of the splitd system (blast-sc2004.pdf) is available at ftp://ftp.ncbi.nlm.nih.gov/blast/documents/. Even though new parameters are added to splitd to enhance the service, most of the parameters remain the same as those used in QBlAst to ensure maximum backward compatibilty.
This document is an update to the previous documentation on QBlAst. It incorporates new parameters added to expand and enhance the BLAST service when splitd was introduced as well as those introduced by the new BLAST pages released on April 17, 2007. Here we describe the steps needed to run BLAST searches through the BLAST URLAPI and the commands available. We will describe each parameter in its own table with actual example showing the way they should appear in the actual URL. We also list corresponding parameters in standalone wwwblast and commandline BLAST, two standalone BLAST binary packages available for download and local installation, under the note section if applicable.