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Protocols

BACTIBASE specifications

Information


Unique identifier OMICS_05726
Name BACTIBASE
Restrictions to use None
Database management system MySQL
Community driven Yes
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Ismail Fliss

Publication for BACTIBASE

BACTIBASE citations

 (11)
library_books

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

2017
PMCID: 5711939
PMID: 29214045
DOI: 10.1038/s41522-017-0042-1

[…] ified ORFs was achieved using a variety of software available at various public databases. Specifically, we used the antimicrobial peptide database, the Antimicrobial Sequence Scanning System (AMPA), BACTIBASE, collection of anti-microbial peptides (CAMP),, and antibacterial peptides (AntiBP). Only ORFs that were predicted to encode putative AMPs within at least two of the utilized databases were […]

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

[…] stigators; 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 as the go-to resources for BGC identification […]

library_books

The sil Locus in Streptococcus Anginosus Group: Interspecies Competition and a Hotspot of Genetic Diversity

2017
Front Microbiol
PMCID: 5222867
PMID: 28119678
DOI: 10.3389/fmicb.2016.02156

[…] teny were manually examined.We searched for each ORF in the non-redundant protein sequences (nr) database with Blastx () to identify putative functions. In addition, each ORF was searched against the BACTIBASE database (, ) of bacteriocins to identify hits with existing bacteriocins. […]

library_books

Discovery of Azurin Like Anticancer Bacteriocins from Human Gut Microbiome through Homology Modeling and Molecular Docking against the Tumor Suppressor p53

2016
Biomed Res Int
PMCID: 4867070
PMID: 27239476
DOI: 10.1155/2016/8490482

[…] acteriocins of our interest, no hits were found, with an exception of p3seq24 from Clostridium hathewayi DSM 13479. The p3seq24 has 37% identities (E-value = 0.002) with Clostridium perfringens UviB (Bactibase ID: BAC090), which is predicted as an antimicrobial and antibacterial bacteriocin. This indicates that all our putative bacteriocins are novel to previously experimentally validated therapeu […]

call_split

A Large Scale Structural Classification of Antimicrobial Peptides

2015
Biomed Res Int
PMCID: 4426897
PMID: 26000295
DOI: 10.1155/2015/475062
call_split See protocol

[…] ADAM contains 7,007 unique AMP sequences extracted from twelve databases (). The twelve databases include APD2 [], AVPpred [], BACTIBASE [], BAGEL3 [], CAMP2 [], DADP [], DAMPD [], HIPdb [], PenBase [], PhytAMP [], RAPD [], and YADAMP []. The AMP sequences in ADAM were mostly derived from natural sources, covering a broad spe […]

library_books

Identification of Multiple Bacteriocins in Enterococcus spp. Using an Enterococcus Specific Bacteriocin PCR Array

2015
PMCID: 5023226
PMID: 27682075
DOI: 10.3390/microorganisms3010001

[…] Bacteriocin genes were found using the online database Bactibase (Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Tunis, Tunisia) [] by searching for individual gene sequences produced by members of the genus, Enterococcus. Duplicates and […]

Citations

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BACTIBASE institution(s)
STELA Dairy Research Center, Nutraceuticals and Functional Foods Institute, Université Laval, Quebec, QC, Canada; Unité de Proteomie Fonctionnelle & Biopreservation Alimentaire, Institut Superieur des Sciences Biologiques Appliquees de Tunis, Universite El Manar, Tunisie

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