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Bacterial Isolate Genome Sequence Database (BIGSdb)

BIGSdb Version 1.23.4

BIGSdb is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

BIGSdb is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Full details of the GNU General Public License can be found at


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Installed plugins

Plugins may be disabled by the system administrator for specific databases where either they're not appropriate or if they may take up too many resources on a public database.

Enabled plugins
BURSTKeith Jolley (University of Oxford, UK)Perform BURST cluster analysis on query results query results1.1.9Limited to queries with between 2 and 1,000 results.
FASTA ExportKeith Jolley (University of Oxford, UK)Export FASTA file of sequences following an allele attribute query2.0.0
Locus ExplorerKeith Jolley (University of Oxford, UK)Tool for analysing allele sequences stored for particular locus1.3.12
Profile ExportKeith Jolley (University of Oxford, UK)Export file of allelic profile definitions following a scheme query1.1.2
Rule QueryKeith Jolley (University of Oxford, UK)Rule-based sequence scanning and reporting1.1.4
Sequence Table ExportKeith Jolley (University of Oxford, UK)Export table of sequences and attributes following an allele attribute query1.1.0
Sequence ComparisonKeith Jolley (University of Oxford, UK)Display a comparison between two sequences1.0.8
Sequence ExportKeith Jolley (University of Oxford, UK)Export concatenated allele sequences in XMFA and FASTA formats1.6.6
Sequence SimilarityKeith Jolley (University of Oxford, UK)Find sequences most similar to selected allele1.1.2
Disabled plugins
NameAuthorDescriptionVersionDisabled because
BLASTKeith Jolley (University of Oxford, UK)BLAST a query sequence against selected isolate data1.4.15Only for isolate databases.
Codon UsageKeith Jolley (University of Oxford, UK)Determine codon usage for specified loci for an isolate database query1.2.10Only for isolate databases.
Unique CombinationsKeith Jolley (University of Oxford, UK)Determine frequencies of unique field combinations1.4.4Only for isolate databases.
Contig exportKeith Jolley (University of Oxford, UK)Analyse and export contigs selected from query results1.1.8Only for isolate databases.
Database FieldsKeith Jolley (University of Oxford, UK)Display description of fields defined for the current database1.0.7Only for isolate databases.
ExportKeith Jolley (University of Oxford, UK)Export dataset generated from query results1.7.9Only for isolate databases.
Field BreakdownKeith Jolley (University of Oxford, UK)Breakdown of query results by field2.2.5Only for isolate databases.
Gene PresenceKeith Jolley (University of Oxford, UK)Analyse presence/absence of loci for dataset generated from query results2.0.7Only for isolate databases.
Genome ComparatorKeith Jolley (University of Oxford, UK)Compare genomes at defined loci or against loci defined in a reference genome2.3.28Only for isolate databases.
GrapeTreeKeith Jolley (University of Oxford, UK)Visualization of genomic relationships1.3.6Only for isolate databases.
iTOLKeith Jolley (University of Oxford, UK)Phylogenetic trees with data overlays1.3.13Only for isolate databases.
MicroreactKeith Jolley (University of Oxford, UK)Open data visualization and sharing for genomic epidemiology1.0.9Only for isolate databases.
PCRKeith Jolley (University of Oxford, UK)In silico PCR tool for designing and testing primers1.0.3Only for isolate databases.
PhyloVizEmmanuel Quevillon (Institut Pasteur, Paris)Creates phylogenetic inference and data visualization for sequence based typing methods1.2.4Only for isolate databases.
PolymorphismsKeith Jolley (University of Oxford, UK)Tool for analysing polymorphic sites for particular locus in an isolate dataset1.1.10Only for isolate databases.
Publication BreakdownKeith Jolley (University of Oxford, UK)Breakdown of query results by publication1.1.9Only for isolate databases.
rMLST species identityKeith Jolley (University of Oxford, UK)Query genomes against rMLST species identifier1.2.7Only for isolate databases.
Sequence Bin BreakdownKeith Jolley (University of Oxford, UK)Breakdown of sequence bin contig properties1.4.6Only for isolate databases.
Two Field BreakdownKeith Jolley (University of Oxford, UK)Two field breakdown1.4.12Only for isolate databases.

Software versions