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PredicTF: a tool to predict bacterial transcription factors in complex microbial communities.

Oliveira Monteiro, L. M.; Saraiva, J. P.; Nunes da Rocha, U.; Brizola Toscan, R.; Stadler, P. F.; Silva-Rocha, R.

2021-01-28 bioinformatics
10.1101/2021.01.28.428666 bioRxiv
Show 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 PredictTFs 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.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.