LABiocin database: A new database designed specifically for Lactic Acid Bacteria bacteriocins.

Bacteriocins from lactic acid bacteria (LAB) are successfully applied as natural alternatives to food preservation and to antibiotics; however, information on these antimicrobial peptides (AMPs) is scattered through the literature and databases. Therefore, we developed the LABiocin database, a specialized database on LAB bacteriocins. The database was stored and compiled using MySQL with NetBeans IDE as the platform. Important data are compiled, including bacteriocin name, class, amino acids and nucleic acid sequences, if available. Target microorganisms, origin, status of the producing strains and their culture conditions and extraction and purification methods are also included in this new database. A phylogenetic tree for the mature peptide bacteriocin sequences has also been created. LABiocin is an interactive database with a user-friendly interface that integrates several tools and services and comprises up to 517 LAB bacteriocins. Besides data searching tools, a BLAST tool was integrated into the database to enable the user to perform a homology search against mature peptide sequences. Users can be linked to other databases that contain additional information, particularly about predicted bacteriocin structure and mechanisms of action. The LABiocin database enables comprehensive functional analysis of this special group of AMPs. This would be useful in food preservation and food safety applications and would also have substantial implications for development of new drugs for medical use. LABiocin database is available at labiocin.net.

ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

PURPOSE: Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. METHODS: ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. RESULTS: A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. CONCLUSIONS: The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field.