Abstract
Transcription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTF’s ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Authors’ email addresses: Lummy Maria Oliveira Monteiro - lummymaria{at}gmail.com, João Saraiva - joao.saraiva{at}ufz.de, Rodolfo Brizola Toscan - rodolfo.toscan{at}ufz.de, Peter F. Stadler - studla{at}bioinf.uni-leipzig.de, Rafael Silva-Rocha - silvarochar{at}usp.br, Ulisses Nunes da Rocha – ulisses.rocha{at}ufz.de
List of Abbreviations
- (TFs)
- Transcription Factors
- (BacTFDB)
- Bacterial Transcription Factor Data Base
- (TFBSs)
- Transcription factor binding sites
- (anammox)
- anaerobic ammonium oxidizing