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Bacterial Isolate Genome Sequence Database (BIGSdb) — BIGSdb 1.16.0 documentation

Installation and configuration of BIGSdb. Submitting data using the submission system. RESTful Application Programming Interface (API). Frequently asked questions (FAQs). Bacterial Isolate Genome Sequence Database (BIGSdb). Bacterial Isolate Genome Sequence Database (BIGSdb). Gene-by-gene population annotation and analysis. The software has been released under the GNU General Public Licence version 3. The latest version of this documentation can be found at http:/ bigsdb.readthedocs.org/. Running the BIG...

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Bacterial Isolate Genome Sequence Database (BIGSdb) — BIGSdb 1.16.0 documentation | bigsdb.readthedocs.io Reviews

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Installation and configuration of BIGSdb. Submitting data using the submission system. RESTful Application Programming Interface (API). Frequently asked questions (FAQs). Bacterial Isolate Genome Sequence Database (BIGSdb). Bacterial Isolate Genome Sequence Database (BIGSdb). Gene-by-gene population annotation and analysis. The software has been released under the GNU General Public Licence version 3. The latest version of this documentation can be found at http:/ bigsdb.readthedocs.org/. Running the BIG...

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1 bigsdb

2 latest

3 concepts and terms

4 bigsdb dependencies

5 database setup

6 administrator’s guide

7 curator’s guide

8 curating submitted data

9 offline curation tools

10 definition downloads

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Bacterial Isolate Genome Sequence Database (BIGSdb) — BIGSdb 1.16.0 documentation | bigsdb.readthedocs.io Reviews

https://bigsdb.readthedocs.io

Installation and configuration of BIGSdb. Submitting data using the submission system. RESTful Application Programming Interface (API). Frequently asked questions (FAQs). Bacterial Isolate Genome Sequence Database (BIGSdb). Bacterial Isolate Genome Sequence Database (BIGSdb). Gene-by-gene population annotation and analysis. The software has been released under the GNU General Public Licence version 3. The latest version of this documentation can be found at http:/ bigsdb.readthedocs.org/. Running the BIG...

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bigsdb.readthedocs.io

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Database setup — BIGSdb 1.17.0 documentation

http://bigsdb.readthedocs.io/en/latest/dbase_setup.html

Installation and configuration of BIGSdb. XML configuration attributes used in config.xml. Isolate database XML attributes. Sequence definition database XML attributes. Over-riding global defaults set in bigsdb.conf. Over-riding values set in config.xml. Setting up the admin user. Submitting data using the submission system. RESTful Application Programming Interface (API). Frequently asked questions (FAQs). There are two types of BIGSdb database:. Sequence definition databases, containing. To create a da...

2

Data analysis plugins — BIGSdb 1.17.0 documentation

http://bigsdb.readthedocs.io/en/latest/data_analysis.html

Installation and configuration of BIGSdb. Scheme and allele breakdown. Analysis using defined loci. Analysis using annotated reference genome. Include in identifiers fieldset. Distance matrix calculation fieldset. Core genome analysis fieldset. Include in results table fieldset. Submitting data using the submission system. RESTful Application Programming Interface (API). Frequently asked questions (FAQs). Click ‘Locus Explorer’ from the sequence definition database contents page. Select the alleles that ...

3

Concepts and terms — BIGSdb 1.17.0 documentation

http://bigsdb.readthedocs.io/en/latest/concepts.html

Installation and configuration of BIGSdb. Submitting data using the submission system. RESTful Application Programming Interface (API). Frequently asked questions (FAQs). BIGSdb is the software platform - not a specific database. There are many instances of BIGSdb databases, so referring to ‘the BIGSdb’ is meaningless. In versions of BIGSdb prior to 1.8.0, an isolate record could only have one live allele. Paralogous loci can be difficult to differentiate by sequence similarity alone. Because of this...

4

RESTful Application Programming Interface (API) — BIGSdb 1.17.0 documentation

http://bigsdb.readthedocs.io/en/latest/rest.html

Installation and configuration of BIGSdb. Submitting data using the submission system. RESTful Application Programming Interface (API). GET / or /db - List site resources. GET /db/{database} - List database resources. GET /db/{database}/loci - List loci. GET /db/{database}/loci/{locus} - Retrieve locus record. GET /db/{database}/loci/{locus}/alleles - Retrieve list of alleles defined for a locus. GET /db/{database}/loci/{locus}/alleles fasta - Download alleles in FASTA format. GET /db/{database}/isolates...

5

Definition downloads — BIGSdb 1.17.0 documentation

http://bigsdb.readthedocs.io/en/latest/data_downloads.html

Installation and configuration of BIGSdb. All loci by scheme. Submitting data using the submission system. RESTful Application Programming Interface (API). Frequently asked questions (FAQs). The sequence definition database defines alleles, i.e. links an allele identifier to a sequence. It also defines scheme, e.g. MLST, profiles. Click the download link for the required locus. Alleles will be downloaded in FASTA format, e.g. FumC 1 GAAGCCTTGGGCGGACGCGATGCCGCCGTTGCCGCTTCGGGCGCATTGAAAACGCTGGCG GCAAGCCTGAA...

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Bacterial Isolate Genome Sequence Database (BIGSdb)

http://usmirror1.pubmlst.org/software/database/bigsdb

Bacterial Isolate Genome Sequence Database (BIGSdb). Gene-by-gene population annotation and analysis. Written by Keith Jolley. 2010-2016 University of Oxford. Jolley and Maiden 2010, BMC Bioinformatics. BIGSdb extends the principle of MLST. BIGSdb runs most of the databases on this site. The software has been released under the GNU General Public Licence version 3. Download BIGSdb releases from. Source code is available from. You can also report bugs or submit enhancement requests here.

pubmlst.org

Bacterial Isolate Genome Sequence Database (BIGSdb)

http://pubmlst.org/software/database/bigsdb

Bacterial Isolate Genome Sequence Database (BIGSdb). Gene-by-gene population annotation and analysis. Written by Keith Jolley. 2010-2016 University of Oxford. Jolley and Maiden 2010, BMC Bioinformatics. BIGSdb extends the principle of MLST. BIGSdb runs most of the databases on this site. The software has been released under the GNU General Public Licence version 3. Download BIGSdb releases from. Source code is available from. You can also report bugs or submit enhancement requests here.

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Bacterial Isolate Genome Sequence Database (BIGSdb) — BIGSdb 1.16.0 documentation

Installation and configuration of BIGSdb. Submitting data using the submission system. RESTful Application Programming Interface (API). Frequently asked questions (FAQs). Bacterial Isolate Genome Sequence Database (BIGSdb). Bacterial Isolate Genome Sequence Database (BIGSdb). Gene-by-gene population annotation and analysis. The software has been released under the GNU General Public Licence version 3. The latest version of this documentation can be found at http:/ bigsdb.readthedocs.org/. Running the BIG...

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