Promotech: a general tool for bacterial promoter recognition

Abstract Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational tools for identifying bacterial promoters have been around for decades. However, most of these tools were designed to recognize promoters in one or few bacter...

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Autores principales:	Ruben Chevez-Guardado, Lourdes Peña-Castillo
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Bacterial promoter Promoter recognition Promoter prediction Machine learning Microbiology Bioinformatics Biology (General) QH301-705.5 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/4c25846f67f044478efda23b23a4ecaf
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id	oai:doaj.org-article:4c25846f67f044478efda23b23a4ecaf
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spelling	oai:doaj.org-article:4c25846f67f044478efda23b23a4ecaf2021-11-21T12:42:00ZPromotech: a general tool for bacterial promoter recognition10.1186/s13059-021-02514-91474-760Xhttps://doaj.org/article/4c25846f67f044478efda23b23a4ecaf2021-11-01T00:00:00Zhttps://doi.org/10.1186/s13059-021-02514-9https://doaj.org/toc/1474-760XAbstract Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational tools for identifying bacterial promoters have been around for decades. However, most of these tools were designed to recognize promoters in one or few bacterial species. Here, we present Promotech, a machine-learning-based method for promoter recognition in a wide range of bacterial species. We compare Promotech’s performance with the performance of five other promoter prediction methods. Promotech outperforms these other programs in terms of area under the precision-recall curve (AUPRC) or precision at the same level of recall. Promotech is available at https://github.com/BioinformaticsLabAtMUN/PromoTech .Ruben Chevez-GuardadoLourdes Peña-CastilloBMCarticleBacterial promoterPromoter recognitionPromoter predictionMachine learningMicrobiologyBioinformaticsBiology (General)QH301-705.5GeneticsQH426-470ENGenome Biology, Vol 22, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Bacterial promoter Promoter recognition Promoter prediction Machine learning Microbiology Bioinformatics Biology (General) QH301-705.5 Genetics QH426-470
spellingShingle	Bacterial promoter Promoter recognition Promoter prediction Machine learning Microbiology Bioinformatics Biology (General) QH301-705.5 Genetics QH426-470 Ruben Chevez-Guardado Lourdes Peña-Castillo Promotech: a general tool for bacterial promoter recognition
description	Abstract Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational tools for identifying bacterial promoters have been around for decades. However, most of these tools were designed to recognize promoters in one or few bacterial species. Here, we present Promotech, a machine-learning-based method for promoter recognition in a wide range of bacterial species. We compare Promotech’s performance with the performance of five other promoter prediction methods. Promotech outperforms these other programs in terms of area under the precision-recall curve (AUPRC) or precision at the same level of recall. Promotech is available at https://github.com/BioinformaticsLabAtMUN/PromoTech .
format	article
author	Ruben Chevez-Guardado Lourdes Peña-Castillo
author_facet	Ruben Chevez-Guardado Lourdes Peña-Castillo
author_sort	Ruben Chevez-Guardado
title	Promotech: a general tool for bacterial promoter recognition
title_short	Promotech: a general tool for bacterial promoter recognition
title_full	Promotech: a general tool for bacterial promoter recognition
title_fullStr	Promotech: a general tool for bacterial promoter recognition
title_full_unstemmed	Promotech: a general tool for bacterial promoter recognition
title_sort	promotech: a general tool for bacterial promoter recognition
publisher	BMC
publishDate	2021
url	https://doaj.org/article/4c25846f67f044478efda23b23a4ecaf
work_keys_str_mv	AT rubenchevezguardado promotechageneraltoolforbacterialpromoterrecognition AT lourdespenacastillo promotechageneraltoolforbacterialpromoterrecognition
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Promotech: a general tool for bacterial promoter recognition

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