Martin Maiden's Research Group

The Bacterial Isolate Genome Sequence Database (BIGSdb) is software designed to store and analyse sequence data for bacterial isolates. Any number of sequences can be linked to isolate records - these can be small contigs assembled from dideoxy sequencing through to whole genomes (complete or multiple contigs generated from parallel sequencing technologies such as 454 or Illumina Solexa). All the functionality of mlstdbnet and agdbnet has been incorporated into BIGSdb and this software will be used to eventually host all the databases on the PubMLST.org site.

BIGSdb runs on Linux systems using the Apache web server and PostgreSQL database.

This is the software that drives many of the publicly available MLST databases on PubMLST.org. The software is derived from the original mlstdb package written by Man-Suen Chan (Chan et al, 2001, Bioinformatics,17, 1077-1083) and released under the GNU General Public Licence.  The new version introduces significant improvements, allowing a distributed database structure.

This program runs on Linux.

Written by Keith Jolley

Jolley et al. (2004) BMC Bioinformatics, 5:86.

This software has been largely superceded by BIGSdb.

The purpose of this program is to bring together some of the analyses that can be performed on MLST data into a single package. The functions of the package can be broadly divided into four categories:

1. Data Summary - allele, profile and polymorphism frequencies, codon usage and GC content.
2. Lineage Assignment - BURST analysis, UPGMA and creation of distance matrices suitable for split decomposition analysis with SplitsTree.
3. Tests for Recombination - Sawyer's Runs Tests, Max Chi Squared, Homoplasy Test and Index of Association.
4. Tests for Selection - dS/dN ratios.

This program runs on Windows.

Written by Keith Jolley.

Jolley et al. (2001) Bioinformatics, 17:1230-1231