About RED-DB

This resource represents a non-redundant repository of resistance gene sequences extracted from public databases of the International Nucleotide Sequence Database Collaboration (EMBL, DDBJ and Genbank nucleotide sequences databases). In the case of gene redundancy, all different organisms where the gene was described are mantained into RED-DB.

Both partial and complete coding sequences are present in the collection. The repository actually contains genes able to confer resistance to the following antibiotics: beta-lactams, glycopeptides, aminoglycosides, tetracyclines, sulphonamides, macrolides, lincosamides, streptogramins b, oxazolidinones and quinolones.

Nomenclature of genes was selected according to the most commonly accepted terms by the scientific community (see the reference section of this website for further details). In addition, genes in RED-DB were clustered based on an arbitrary selected cut-off of 70% DNA identity using the blastclust tool from the stand-alone NCBI blast suite. Clusters allow the user to easily search RED-DB.

New Homologous genes are appended in RED-DB, on a monthly basis, by an automatic procedure that identifies candidates using the BLAST software and imports them in the database, if not already present. After each update, RED-DB curators apply the most appropriate name for each newly inserted gene.

RED-DB can be searched either by a text- or a cluster-based approach, to retrieve protein or nucleotide sequences.
TEMPOTest-QC project