Basic Overview

• What is BLAST?
• What is the BLAST 2.0 Server?
• What are Gapped and PSI-BLAST?
• What are the BLAST network clients?
• How can I access the BLAST services at NCBI?

 

 

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 simple BLAST tutorial located under the Education link in the sidebar of the NCBI home page (http://www.ncbi.nlm.nih.gov/).

Q: What is the BLAST 2.0 Server?

The BLAST 2.0 search engine has been designed for optimal speed and sensitivity. The software behind BLAST version 2.0 was written from scratch to allow BLAST to handle the new challenges posed by the sequence databases in the coming years.

Improvements of BLAST version 2.0 over 1.4 of interest to all users are:

- Gapped alignments.

- Master-slave display options for the alignments

- Organism specific BLAST.

- Position-specific-iterated searches with PSI-BLAST (Altschul et al., 1997).
 

Q: What are Gapped BLAST and PSI-BLAST?

Gapped BLAST and PSI-BLAST are useful search tools provided by the BLAST server (version 2.0) (Altschul et al., 1997).

The Gapped BLAST algorithm allows gaps (deletions and insertions) to be introduced into the alignments that are returned. Allowing gaps means that similar regions are not broken into several segments. The scoring of these gapped alignments tends to reflect biological relationships more closely.

Position-Specific Iterated BLAST (PSI-BLAST) provides an automated, easy-to-use version of a "profile" search, which is a sensitive way to look for sequence homologues. The program first performs a gapped BLAST database search. The PSI-BLAST program uses the information from any significant alignments returned to construct a position-specific score matrix, which replaces the query sequence for the next round of database searching. PSI-BLAST may be iterated until no new significant alignments are found. At this time PSI-BLAST may be used only for comparing protein queries with protein databases.

Q: What is the network BLAST client?

A network client is software installed on your local machine that communicate across the network with a distant server. The BLAST network clients are able to process the search results in new useful ways because of the use of the ASN.1 data model. (Madden et al, 1996).

Blastcl3is the standard network BLAST client at this point in time. Blastcl3 can search all the sequences in a FASTA file, produce one-to-many (master-slave) alignments as well as HTML, and it can perform searches against multiple databases.  Organism-specific searches are planned for the near future.  A full list of command-line options is given below. It provides output in HTML format, encryption, and 'dust' filtering of nucleotide sequences for low-complexity regions. The blastcl3 supports full BLAST 2.0 alignments and currently supports the BLAST 2.0.9 algorithm. You can download blastcl3 form the anonymous FTP location ftp://ncbi.nlm.nih.gov/blast/network/netblast/.
 
 

Q: How can I access the NCBI's BLAST services?

There are four basic 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. These include gapped and iterative BLAST searches as well as searches of several specialized data sets made available by different sequencing centers. The exact URL's and the form of the BLAST pages are not guaranteed to be unchanged over time.

NCBI provides a stable URL that may be used to perform BLAST searches from another program (i.e., without interactive use of a Web browser). A demonstration client (ftp://ncbi.nlm.nih.gov/blast/blasturl/) and a README demonstrate how to access this URL.

Network BLAST:

Blastcl3is the standard network BLAST client at this point in time. You can download blastcl3 form the anonymous FTP location ftp://ncbi.nlm.nih.gov/blast/network/netblast/.

Standalone BLAST:

BLAST 2.0 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 IRIX6.2, Solaris2.5, DEC OSF1 (ver.4), and Win32 systems. BLAST 2.0 executables may be found on the NCBI anonymous FTP server (ftp://ncbi.nlm.nih.gov) under /blast/executables/. Please read the README file in this directory for more information. You can also find this document on the web page http://www.ncbi.nlm.nih.gov/BLAST/newblast.html#standalone.

There is also some information on setting up the programs at the NHGRI site at:

http://genome.nhgri.nih.gov/blastall/blast_install
 

E-Mail Server:

The NCBI BLAST Email server is the best option for people without convenient access to the Web. A similarity search can be performed by sending a properly formatted mail message containing the nucleotide or protein query sequence to blast@ncbi.nlm.nih.gov. The query sequence is compared against the specified database using the BLAST algorithm and the results are returned in an email message. For more information on formulating email BLAST searches, please send a message consisting of the word HELP to the same address, blast@ncbi.nlm.nih.gov.