Sowdhamini, R. | bioRxiv Science

bioRxiv2018

EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins

BackgroundThe repertoire of RNA-binding proteins (RBPs) in bacteria play crucial role for their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism into a comprehensive database named EcRBPome.\n\nResultsEcRBPome contains RBPs recorded from 166 complete E. coli proteomes available in the RefSeq database (as of May 2016). The database provides various features related to the E. coli RBPs, like their domain architectures, PDB structures, GO and EC annotations etc. It provides the assembly, bioproject and biosample details of each strain, as well as cross-strain comparison of occurrences of various RNA-binding domains (RBDs). The percentage of RBPs, the abundance of the various RBDs harboured by each strain have been graphically represented in this database and available alongside other files for user download.\n\nConclusionTo the best of our knowledge, this is the first database of its kind and we hope that it will be of great use to the biological community. Database URL: http://caps.ncbs.res.in/ecrbpome

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bioRxiv2018

hRBPome: a central repository of all known human RNA-binding proteins

BackgroundRNA-binding proteins (RBPs) have been extensively studied in humans over the past few years. Multiple reports have been made in the literature for genome-wide survey for this class of proteins in the human genome using different tools and techniques. Due to the inherent difference in the nature of the methods used in identifying human RBPs, as well as the diverse sources for data collection in each of these studies, there exists immense heterogeneity (including diversity in data formats) and poor intersection among the datasets available from the different studies.\n\nDescriptionhRBPome is a comprehensive database of human RBPs known from six different studies. We have introduced considerable uniformity in the data, by mapping the various data formats reported by the different studies to gene names. This makes comparison across studies (datasets) easier than was possible before. We also provide confidence scores to each of these known RBPs, on the basis of their presence across studies.\n\nConclusionThis database presents a set of 837 high confidence RBP genes, identified in three or more resources, out of the six studies considered. Hence, it forms a \"gold standard\" for RBPs in the human genome. It also provides information for all the human RBPs from multiple resources, known to the best of our knowledge, on a common platform. The database can be accessed from the following URL: http://caps.ncbs.res.in/hrbpome

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