Basic Overview

• What is BLAST?
• What is the best BLAST for me?
• 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 that seeks local as opposed to global alignments and is therefore able to detect relationships among sequences that 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 the Best BLAST for me?

There are many different types of BLAST available from the main BLAST web page. Choosing the right one depends on the type of sequence you are searching with (long, short; nucleotide protein), and the desired database. In order to help guide you to the right service for your search please consult the "BLAST Program Selection Guide".

This guide provides information on what database and BLAST service (megaBLAST, translation BLAST etc) is ideal for your search. Plus there is also additional information describing how the tools work and why they are best for certain types of searches.

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:

Network BLAST:

BLAST URL API

The BLAST URL API 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 that passes sequences to the NCBI databases and return results locally. There are many features:

• 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 to run scripts.

Instructions for the URL API are located in three formats: HTML, PDF, and PostScript.