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This is the development version of planttfhunter; for the stable release version, see planttfhunter.

Identification and classification of plant transcription factors

Bioconductor version: Development (3.20)

planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.

Author: Fabrício Almeida-Silva [aut, cre] , Yves Van de Peer [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at>

Citation (from within R, enter citation("planttfhunter")):


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Genome-wide identification and classification of transcription factors in plant genomes HTML R Script
Reference Manual PDF


biocViews Classification, FunctionalGenomics, FunctionalPrediction, GenomeAnnotation, HiddenMarkovModel, Sequencing, Software, Transcription
Version 1.5.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports Biostrings, SummarizedExperiment, utils, methods
System Requirements HMMER
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