ApicoTFdb: The comprehensive web repository of apicomplexan transcription factors and regulators

Abstract Despite significant progress in apicomplexans genome sequencing and genomics, the current list of experimentally validated TFs in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and TAFs. We have performed systematic bioinformatics aided prediction of TFs and TAFs in apicomplexan genomes, and developed ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TAFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1310 TFs, out of which 833 are novel and computationally predicted TFs, representing 22 distinct families across 14 apicomplexan species. The predictions include TFs of TUB, NAC, BSD, CCAAT, HTH, Cupin/Jumonji, winged-helix, and FHA family proteins, not reported earlier in the genomes. Apart from TFs, ApicoTFdb also classifies TAFs into three main subclasses-TRs, CRRs and RNARs, representing 3047 TAFs in 14 apicomplexan species are analyzed in this study. The database is equipped with a set of useful tools for comparative analysis of a user-defined list of the proteins. ApicoTFdb will be useful to the researchers interested in less-studied gene regulatory mechanisms mediating the complex life cycle of the apicomplexan parasites. The database will aid the discovery of novel drug targets to much needed combat the growing drug resistance in the parasites.