BLAST Overview

Basic Overview

What is BLAST? What is Q BLAST? How can I access the BLAST services at NCBI? What is the Standalone WWW BLAST Server?

Q: What is BLAST? BLAST® (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. The BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity to distant sequence relationships. The scores assigned in a BLAST search have a well-defined statistical interpretation, making real matches easier to distinguish from random background hits. BLAST uses a heuristic algorithm which seeks local as opposed to global alignments and is therefore able to detect relationships among sequences which share only isolated regions of similarity (Altschul et al., 1990). For a better understanding of BLAST you can refer to the BLAST Course which explains the basics of the BLAST algorithm. There is also a description of BLAST services located here. Also for details on BLAST and theory of similarity search, see the references section.

Q: What is "QBLAST" NCBI introduced the new queuing system to BLAST that allows users to retrieve results at their convenience and format their results multiple times with different formatting options. This system reduces the number of simultaneous connections to the NCBI Web servers, permitting all NCBI services to respond even faster. It also allows the NCBI to more efficiently use computational resources, better serving the community. With "QBLAST" All searches submitted to the servers are issued a Request ID (RID). When you click the button, a separate status screen will appear which will tell you the time the search was submitted and the time till the next check for your completed search. When the search is completed the results will automatically appear in the new screen. RIDs can be retrieved at anytime and reformatted without having to rerun the search. RIDs will generally be available for a 24 hour period before being purged from the servers.

Q: How can I access the NCBI's BLAST services? There are four ways to use BLAST services: WWW BLAST: The easiest way to use BLAST is through the Web. Users may simply point their browsers at the NCBI home page (http://www.ncbi.nlm.nih.gov) and link to the /BLAST pages for any number of different types of searches. A complete description of BLAST services is available at this location.

Standalone BLAST: BLAST can be run locally as a full executable and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. BLAST binaries are provided for Macintosh, Win32 (PC), LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP UX systems. Standalone BLAST executables may be found on the NCBI anonymous FTP server (ftp://ftp.ncbi.nih.gov/) under /blast/executables/. Please read the README file in this directory for more information. There is also some information on setting up Standalone BLAST at the NHGRI site at: http://genome.nhgri.nih.gov/blastall/blast_install

Network BLAST: Blastcl3 is the NCBI BLAST network client. It allows remote TCP/IP connections to the NCBI BLAST servers in order to run BLAST searches. No web browser is required. The BLAST network client can also be used to "batch" search many sequences against the NCBI databases at one time. You can download blastcl3 from the anonymous FTP location ftp://ftp.ncbi.nih.gov/blast/network/netblast/CURRENT/.

BLAST URL API The BLAST URL API The URLAPI is a standardized application program interface (API) for accessing the NCBI QBLAST system. It uses direct HTTP-encoded requests to NCBI web server. The URL API will allow you to write a script which passes sequences to the NCBI databases and return results locally. Features include: it does not require the download of an executable from NCBI ftp site there is no need download database files from NCBI to your local machine the URL API is easy to maintain and keep backward compatible it is not necessary to hack the NCBI BLAST CGI in order to run scripts Instructions for the URL API are located in three formats: HTML, PDF, and PostScript.

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Revised March 19, 2002