BACTIBASE second release: a database and tool platform for bacteriocin characterization

By Riadh Hammami, Abdelmajid Zouhir, C. Le Lay, J. Ben Hamida, Ismail Fliss. BMC Microbiology, 2010

328 citations recorded by the source corpus.

BackgroundBACTIBASE is an integrated open-access database designed for the characterization of bacterial antimicrobial peptides, commonly known as bacteriocins.DescriptionFor its second release, BACTIBASE has been expanded and equipped with additional functions aimed at both casual and power users. The number of entries has been increased by 44% and includes data collected from published literature as well as high-throughput datasets. The database provides a manually curated annotation of bacteriocin sequences. Improvements brought to BACTIBASE include incorporation of various tools for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modelling and retrieval through our taxonomy Browser.ConclusionThe provided features should make BACTIBASE a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use. BACTIBASE is available at http://bactibase.pfba-lab-tun.org.

Subfields: Food Science, Microbiology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/9d9518295d5ed42688c693032fc91f6d123de503

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Citations in the corpus

LAMP: A Database Linking Antimicrobial Peptides (2013, methodology): “Other databases are more specialized and have focused to AMPs produced only by bacteria (BACTIBASE [18]), plants (PhytAMP [19]), shrimp (PenBase [20]), synthetic method (SAPD [21,22]) and recombinant methods (RAPD [21]).”
Prokaryotic antimicrobial peptides (2011, background): “Development of in silico approaches to identify bacteriocin operons is becoming available, including bacteriocin databases (de Jong et al. 2006, 2010; Hammami et al. 2010).”
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides (2015, background): “BACTIBASE 228 72 Presenta Bacteriocins (32) YADAMP 2525 Presenta Absent General (33) PhytAMP 273 39 Presenta Plant AMPs (34) Peptaibiotics database 1344 Absent Absent Peptaibols (35)”
BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides (2013, unknown): “Other useful tools have also been developed, such as the data repository Bactibase (15) and the prediction tool antiSMASH (16), which also supports non-ribosomal peptides but lacks some of the classes supported by the faster BAGEL3.”
MilkAMP: a comprehensive database of antimicrobial peptides of dairy origin (2014, background): “…category of peptide (Defensins Knowledgebase (Seebah et al. 2007), Peptaibol Database (Whitmore and Wallace 2004), etc.) or phylogenetic origin (PhytAMP (Hammami et al. 2009), BACTIBASE (Hammami et al. 2010), PenBase (Gueguen et al. 2006), etc.), as previously reviewed (Hammami and Fliss 2010).”
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins (2018, background): “They all depend on information from literature and databases such as bactibase (12) CAMPR3 (13) and the MiBig data repository (14).”