AgdbNet

Version 1.0.0

Released: 2006-03-29
Written by Keith Jolley, © 2006 University of Oxford

Jolley & Maiden 2006, BMC Bioinformatics, 7:314.

AgdbNet is antigen sequence database software for web-based bacterial typing. The software facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. It's written in Perl and runs on Linux/UNIX systems.

Databases are described by XML files and can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The databases can optionally have integral isolate tables so that information about representative isolates can be retrieved or they may be configured to query external isolate databases, such as those hosted on PubMLST.org.

The software is used on a number of public bacterial typing databases:

Screenshots

Click images to enlarge.

Neisseria meningitidis PorA VR databaseResults of a search of the S. equi database
Neisseria meningitidis PorA variable region databaseStreptococcus equi seM database

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License

AgdbNet is open-source software, published under the GNU General Public License.

Obtaining the software

Download and installation guide

Please contact Keith Jolley if you have any problems installing agdbNet.