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Bacterial Isolate Genome Sequence Database (BIGSdb)

BIGSdb Version 1.17.2

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 http://www.gnu.org/licenses/gpl.html.

Documentation

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
NameAuthorDescriptionVersionComments
BURSTKeith Jolley (University of Oxford, UK)Perform BURST cluster analysis on query results query results1.1.3Limited to queries with between 2 and 1000 results.
Codon UsageKeith Jolley (University of Oxford, UK)Determine codon usage for specified loci for an isolate database query1.2.4
Unique CombinationsKeith Jolley (University of Oxford, UK)Determine frequencies of unique field combinations1.1.2
Database FieldsKeith Jolley (University of Oxford, UK)Display description of fields defined for the current database1.0.4
ExportKeith Jolley (University of Oxford, UK)Export dataset generated from query results1.3.10
Field BreakdownKeith Jolley (University of Oxford, UK)Breakdown of query results by field1.2.1
PhyloTreeKeith Jolley (University of Oxford, UK)Generate phylogenetic trees1.1.0Limited to queries with between 2 and 2000 results.
PhyloVizEmmanuel Quevillon (Institut Pasteur, Paris)Creates phylogenetic inference and data visualization for sequence based typing methods1.0.0Limited to queries with between 2 and 10000 results.
PolymorphismsKeith Jolley (University of Oxford, UK)Tool for analysing polymorphic sites for particular locus in an isolate dataset1.1.3Limited to queries with fewer than 2000 results.
Presence/AbsenceKeith Jolley (University of Oxford, UK)Analyse presence/absence status of loci for dataset generated from query results1.1.6
Publication BreakdownKeith Jolley (University of Oxford, UK)Breakdown of query results by publication1.1.5
Scheme BreakdownKeith Jolley (University of Oxford, UK)Breakdown of scheme fields and alleles1.1.7
Sequence ExportKeith Jolley (University of Oxford, UK)Export concatenated allele sequences in XMFA and FASTA formats1.5.12
Two Field BreakdownKeith Jolley (University of Oxford, UK)Two field breakdown1.4.1
Disabled plugins
NameAuthorDescriptionVersionDisabled because
BLASTKeith Jolley (University of Oxford, UK)BLAST a query sequence against selected isolate data1.4.2Not specifically enabled for this database.
Contig exportKeith Jolley (University of Oxford, UK)Analyse and export contigs selected from query results1.1.1Not specifically enabled for this database.
FASTA ExportKeith Jolley (University of Oxford, UK)Export FASTA file of sequences following an allele attribute query1.0.1Only for seqdef databases.
Genome ComparatorKeith Jolley (University of Oxford, UK)Compare genomes at defined loci or against loci defined in a reference genome2.0.5Not specifically enabled for this database.
Locus ExplorerKeith Jolley (University of Oxford, UK)Tool for analysing allele sequences stored for particular locus1.3.5Only for seqdef databases.
Rule QueryKeith Jolley (University of Oxford, UK)Rule-based sequence scanning and reporting1.1.1Only for seqdef databases.
Sequence Table ExportKeith Jolley (University of Oxford, UK)Export table of sequences and attributes following an allele attribute query1.0.1Only for seqdef databases.
Sequence Bin BreakdownKeith Jolley (University of Oxford, UK)Breakdown of sequence bin contig properties1.4.0Not specifically enabled for this database.
Sequence ComparisonKeith Jolley (University of Oxford, UK)Display a comparison between two sequences1.0.6Only for seqdef databases.
Sequence SimilarityKeith Jolley (University of Oxford, UK)Find sequences most similar to selected allele1.1.0Only for seqdef databases.
Tag StatusKeith Jolley (University of Oxford, UK)Breakdown status of sequence tagging and designation by locus1.2.1Not specifically enabled for this database.

Software versions