Supported Applications

Description

(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

Usage

Usage Notes

Full Blast database documentation is here: ftp://ftp.ncbi.nlm.nih.gov/blast/db/blastdb.html

The Blast developers suggest using Blast+ instead of Blast as "the Blast+ applications have a number of performance and feature improvements over the legacy BLAST applications".

Pre-formatted databases must be downloaded using the update_blastdb.pl script or via FTP in binary mode. Documentation for the update_blastdb.pl script can be obtained by running the script without any arguments (perl is required).

The compressed files downloaded must be inflated with gzip or other decompress tools. The BLAST database files can then be extracted out of the resulting tar file using tar program on Unix/Linux or WinZip and StuffIt Expander on Windows and Macintosh platforms, respectively.

Large databases are formatted in multiple 1 Gigabytes volumes, which are named using the database.##.tar.gz convention. All relevant volumes are required. An alias file is provided so that the database can be called using the alias name without the extension (.nal or .pal). For example, to call est database, simply use "-d est" option in the commandline (without the quotes).

Certain databases are subsets of a larger parental database. For those databases, alias and mask files, rather than actual databases, are provided. The mask file needs the parent database to function properly. The parent databases should be generated on the same day as the mask file. For example, to use swissprot pre-formatted database, swissprot.tar.gz, one will need to get the nr.tar.gz with the same date stamp.

Installation

Primary Citation*

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J Mol Biol. 215(3): 403-410.

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