Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes

DNA-binding transcription factors (TFs) play a central role in the gene expression of all organisms, from viruses to humans, including bacteria and archaea. The role of these proteins is the fate of gene expression in the context of environmental challenges. Because thousands of genomes have been sequenced to date, predictions of the encoded proteins are validated through the use of bioinformatics tools to obtain the necessary experimental, posterior knowledge. In this chapter, we describe three approaches to identify TFs in protein sequences. The first approach integrates the results of sequence comparisons and PFAM assignments, using as reference a manually curated collection of TFs. The second approach considers the prediction of DNA-binding structures, such as the classical helix-turn-helix (HTH); and the third approach considers a deep learning model. We suggest that all approaches must be considered together to increase the possibility of identifying new TFs in bacterial and archaeal genomes.