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Protocols

BAGEL specifications

Information


Unique identifier OMICS_06344
Name BAGEL
Interface Web user interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Anne de Jong
  • person_outline Oscar Kuipers

Additional information


http://bagel4.molgenrug.nl/help.php

Information


Unique identifier OMICS_06344
Name BAGEL
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A folder containing one or multiple DNA files (files containing multiple DNA entries are allowed).
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Anne de Jong
  • person_outline Oscar Kuipers

Additional information


http://bagel4.molgenrug.nl/help.php

Publications for BAGEL

BAGEL citations

 (12)
library_books

Complete genome sequence of Lactobacillus rhamnosus Pen, a probiotic component of a medicine used in prevention of antibiotic associated diarrhoea in children

2018
PMCID: 5822663
PMID: 29483943
DOI: 10.1186/s13099-018-0235-z

[…] sus Pen were individually search against Conserved Domains Database (NCBI) [] and InterPro detabase (EMBL-EBI) []. Genes potentially involved in the biosynthesis of bacteriocins were identified using BAGEL []. The presence of antibiotic resistance genes was tested using ResFinder []. Phaster was used to search for prophage sequences [] and the presence of a CRISPR/Cas system was predicted using CR […]

library_books

Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory

2017
Genome Announc
PMCID: 5658498
PMID: 29074660
DOI: 10.1128/genomeA.01172-17

[…] ns 3,525 genes, 3,361 proteins, 43 pseudogenes, 32 rRNAs, 89 tRNAs, 4 putative phages, and 5 clustered regularly interspaced short palindromic repeat (CRISPR)-associated repeat regions. Additionally, BAGEL3 () predicts the presence of a novel circularin-like bacteriocin with a 46% identity to circularin A (), as determined by pairwise alignment using BLASTp (). AntiSMASH v4.0.2 () also highlighted […]

library_books

Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials

2017
Mar Drugs
PMCID: 5618411
PMID: 28846659
DOI: 10.3390/md15090272

[…] functions as a useful access point for investigators; containing website links to databases and tools used in genome mining and secondary metabolism research []. Automated tools such as antiSMASH [] BAGEL [] and PRISM [] and databases such as Bactibase [] ClusterMine360 [] and MIBiG [] represent just a few of the sophisticated in silico analytical tools which have quickly established themselves a […]

library_books

Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics

2017
PLoS One
PMCID: 5495459
PMID: 28671965
DOI: 10.1371/journal.pone.0180493

[…] me plot was generated with DNAPlotter []. The origin of chromosomal replication was predicted with the Ori-Finder tool []. Genomic islands were searched for with IslandViewer [] and bacteriocins with BAGEL3 []. […]

library_books

A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus☆

2016
PMCID: 5640789
PMID: 29062941
DOI: 10.1016/j.synbio.2016.05.001

[…] ein length diversity was not less than 0.5. Potential specialized metabolite gene clusters of all 18 Amycolatopsis genomes that have been predicted using antiSMASH 3. RiPPs analysis were predicted by BAGEL3 .Circular map, comparative analysis and assignment of common orthologues: Genome circular maps were generated using GenomeViz and DNAplotter . Comparative analyses of genomes from strains clas […]

library_books

Genomic Diversity of Enterotoxigenic Strains of Bacteroides fragilis

2016
PLoS One
PMCID: 4922554
PMID: 27348220
DOI: 10.1371/journal.pone.0158171

[…] using an Illumina MiSeq sequencer. Sequences were annotated using RAST software and software developed by ChunLab. Genome comparisons were performed using Mauve [], RAST/SEED server [], ResFinder [], BAGEL [], PHAST [] and CLGenomics software. The genome sequences have been deposited at GenBank under the accession numbers LIDV00000000 (2-078382-3), LIDT00000000 (20793–3), LIDU00000000 (20656-2-1), […]

Citations

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BAGEL institution(s)
Molecular Genetics, GBB, University of Groningen, Groningen, the Netherlands
BAGEL funding source(s)
Supported by the EU Horizon 2020 Rafts4Biotech (grant agreement No 720776) project; Dutch NWO-TTW program Back to the Roots; and Netherlands Organisation for Scientific Research [NWO, ALWOP.214].

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