PredicTF

PredicTF predicts and classifies bacterial transcription factors in genomes, metagenomes, and metatranscriptomes to characterize regulatory proteins within complex microbial communities.

Key Features:

• Prediction and Classification: PredicTF identifies and classifies transcription factors from bacterial genomic, metagenomic, and metatranscriptomic sequence data.
• Two-step Evaluation on Environmental Samples: The method was evaluated first on the genome of an environmental isolate and then applied to metagenomic data and 11 metatranscriptomes from an anaerobic ammonium oxidation (anammox) bioreactor.

Scientific Applications:

• Microbial ecology and regulatory network analysis: Prediction of TFs in isolate genomes and complex metagenomic/metatranscriptomic datasets to support inference of regulatory networks in microbial communities.
• Study of anaerobic ammonium oxidation (anammox): Identification of TFs involved in anammox in bioreactor communities using metagenomes and 11 metatranscriptomes.

Methodology:

Performance was assessed via a two-step evaluation consisting of validation on an environmental isolate genome followed by application to metagenomes and 11 metatranscriptomes from an anammox bioreactor.