Bacterial Isolate Genome Sequence Database (BIGSdb)
Version 1.6.1
Written by Keith Jolley
Copyright © University of Oxford, 2010-2013.
Jolley & Maiden BMC Bioinformatics 2010, 11:595
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.
Details of this software and the latest version can be downloaded from http://pubmlst.org/software/database/bigsdb/.
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 | ||||
|---|---|---|---|---|
| Name | Author | Description | Version | Comments |
| BURST | Keith Jolley (University of Oxford, UK) | Perform BURST cluster analysis on query results query results | 1.0.3 | Limited to queries with between 2 and 1000 results. |
| Concatenate | Keith Jolley (University of Oxford, UK) | Concatenate allele sequences from dataset generated from query results | 1.2.1 | |
| FASTA Export | Keith Jolley (University of Oxford, UK) | Export FASTA file of sequences following an allele attribute query | 1.0.0 | |
| Locus Explorer | Keith Jolley (University of Oxford, UK) | Tool for analysing allele sequences stored for particular locus | 1.1.1 | |
| Rule Query | Keith Jolley (University of Oxford, UK) | Rule-based sequence scanning and reporting | 1.0.1 | |
| Sequence Comparison | Keith Jolley (University of Oxford, UK) | Display a comparison between two sequences | 1.0.3 | |
| Sequence Similarity | Keith Jolley (University of Oxford, UK) | Find sequences most similar to selected allele | 1.0.2 | |
| Xmfa Export | Keith Jolley (University of Oxford, UK) | Export allele sequences in XMFA format | 1.4.1 | |
| Disabled plugins | ||||
| Name | Author | Description | Version | Disabled because |
| BLAST | Keith Jolley (University of Oxford, UK) | BLAST a query sequence against selected isolate data | 1.1.2 | Only for isolate databases. |
| Codon Usage | Keith Jolley (University of Oxford, UK) | Determine codon usage for specified loci for an isolate database query | 1.1.3 | Only for isolate databases. |
| Unique Combinations | Keith Jolley (University of Oxford, UK) | Determine frequencies of unique field combinations | 1.0.4 | Only for isolate databases. |
| Contig export | Keith Jolley (University of Oxford, UK) | Analyse and export contigs selected from query results | 1.0.0 | Only for isolate databases. |
| Database Fields | Keith Jolley (University of Oxford, UK) | Display description of fields defined for the current database | 1.0.1 | Only for isolate databases. |
| Export | Keith Jolley (University of Oxford, UK) | Export dataset generated from query results | 1.1.1 | Only for isolate databases. |
| Field Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of query results by field | 1.0.3 | Only for isolate databases. |
| Genome Comparator | Keith Jolley (University of Oxford, UK) | Compare genomes at defined loci or against loci defined in a reference genome | 1.5.5 | Only for isolate databases. |
| Polymorphisms | Keith Jolley (University of Oxford, UK) | Tool for analysing polymorphic sites for particular locus in an isolate dataset | 1.0.2 | Only for isolate databases. |
| Presence/Absence | Keith Jolley (University of Oxford, UK) | Analyse presence/absence status of loci for dataset generated from query results | 1.1.0 | Only for isolate databases. |
| Publication Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of query results by publication | 1.1.1 | Only for isolate databases. |
| Scheme Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of scheme fields and alleles | 1.1.2 | Only for isolate databases. |
| Sequence Bin Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of sequence bin contig properties | 1.0.6 | Only for isolate databases. |
| Tag Status | Keith Jolley (University of Oxford, UK) | Breakdown status of sequence tagging and designation by locus | 1.1.0 | Only for isolate databases. |
| Two Field Breakdown | Keith Jolley (University of Oxford, UK) | Two field breakdown | 1.1.1 | Only for isolate databases. |