BRONX: Barcode Recognition Obtained with Nucleotide eXposés

Damon P. Little1

1Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, NY, USA

version 2.0

An updated version of this script is now available. Most users should use the newer, faster, and more portable version.


This pair of scripts is designed to transform a set of FASTA formated sequences into a queriable BRONX reference database for DNA barcoding. To create the database structure and MySQL user required for BRONX, first run “mysql -u root -p < mysql.sql”. WARNING: this will delete all data in an existing BRONX database.

script usage

(1) in_file

The “in_file” is assumed to be DNA sequences in FASTA format. Labels must begin with a unique identifier followed by an underscore and seven taxonomic descriptors (e.g. kingdom, division, class, order, family, genus, and species) ordered from the most inclusive to the least inclusive. Identifiers are separated by underscores. Empty identifiers are allowed. Unique identifiers can be automatically assigned using “NO-UNIQUE-IDENTIFIER” for the identifier string. Identifiers/names already existing in the database will be updated with the new sequence and taxonomy.

The file “sample.fasta” contains reference sequences that can be processed into a BRONX database (“sample.mysql” contains the database dump).

(2) in_file

The “in_file” is assumed to be DNA sequences in FASTA format.


PERL interpreter


Little, D. P. 2009. BRONX: Barcode Recognition Obtained with Nucleotide eXposés. Program distributed by the author.

Little, D. P. 2011. DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS ONE. 6 (8): e20552.