Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations
ABSTRACT The promoter region is a key element required for the production of RNA in bacteria. While new high-throughput technology allows massively parallel mapping of promoter elements, we still mainly rely on bioinformatics tools to predict such elements in bacterial genomes. Additionally, despite...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2020-08-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSystems.00439-20 |
| _version_ | 1818386144390283264 |
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| author | Murilo Henrique Anzolini Cassiano Rafael Silva-Rocha |
| author_facet | Murilo Henrique Anzolini Cassiano Rafael Silva-Rocha |
| author_sort | Murilo Henrique Anzolini Cassiano |
| collection | DOAJ |
| description | ABSTRACT The promoter region is a key element required for the production of RNA in bacteria. While new high-throughput technology allows massively parallel mapping of promoter elements, we still mainly rely on bioinformatics tools to predict such elements in bacterial genomes. Additionally, despite many different prediction tools having become popular to identify bacterial promoters, no systematic comparison of such tools has been performed. Here, we performed a systematic comparison between several widely used promoter prediction tools (BPROM, bTSSfinder, BacPP, CNNProm, IBBP, Virtual Footprint, iPro70-FMWin, 70ProPred, iPromoter-2L, and MULTiPly) using well-defined sequence data sets and standardized metrics to determine how well those tools performed related to each other. For this, we used data sets of experimentally validated promoters from Escherichia coli and a control data set composed of randomly generated sequences with similar nucleotide distributions. We compared the performance of the tools using metrics such as specificity, sensitivity, accuracy, and Matthews correlation coefficient (MCC). We show that the widely used BPROM presented the worse performance among the compared tools, while four tools (CNNProm, iPro70-FMWin, 70ProPred, and iPromoter-2L) offered high predictive power. Of these tools, iPro70-FMWin exhibited the best results for most of the metrics used. We present here some potentials and limitations of available tools, and we hope that future work can build upon our effort to systematically characterize this useful class of bioinformatics tools. IMPORTANCE The correct mapping of promoter elements is a crucial step in microbial genomics. Also, when combining new DNA elements into synthetic sequences, predicting the potential generation of new promoter sequences is critical. Over the last years, many bioinformatics tools have been created to allow users to predict promoter elements in a sequence or genome of interest. Here, we assess the predictive power of some of the main prediction tools available using well-defined promoter data sets. Using Escherichia coli as a model organism, we demonstrated that while some tools are biased toward AT-rich sequences, others are very efficient in identifying real promoters with low false-negative rates. We hope the potentials and limitations presented here will help the microbiology community to choose promoter prediction tools among many available alternatives. |
| first_indexed | 2024-12-14T03:49:23Z |
| format | Article |
| id | doaj.art-93812e5b99c34489b76ff7b8aafe4c3f |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-14T03:49:23Z |
| publishDate | 2020-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-93812e5b99c34489b76ff7b8aafe4c3f2022-12-21T23:18:15ZengAmerican Society for MicrobiologymSystems2379-50772020-08-015410.1128/mSystems.00439-20Benchmarking Bacterial Promoter Prediction Tools: Potentialities and LimitationsMurilo Henrique Anzolini Cassiano0Rafael Silva-Rocha1FMRP - University of São Paulo, Ribeirão Preto, SP, BrazilFMRP - University of São Paulo, Ribeirão Preto, SP, BrazilABSTRACT The promoter region is a key element required for the production of RNA in bacteria. While new high-throughput technology allows massively parallel mapping of promoter elements, we still mainly rely on bioinformatics tools to predict such elements in bacterial genomes. Additionally, despite many different prediction tools having become popular to identify bacterial promoters, no systematic comparison of such tools has been performed. Here, we performed a systematic comparison between several widely used promoter prediction tools (BPROM, bTSSfinder, BacPP, CNNProm, IBBP, Virtual Footprint, iPro70-FMWin, 70ProPred, iPromoter-2L, and MULTiPly) using well-defined sequence data sets and standardized metrics to determine how well those tools performed related to each other. For this, we used data sets of experimentally validated promoters from Escherichia coli and a control data set composed of randomly generated sequences with similar nucleotide distributions. We compared the performance of the tools using metrics such as specificity, sensitivity, accuracy, and Matthews correlation coefficient (MCC). We show that the widely used BPROM presented the worse performance among the compared tools, while four tools (CNNProm, iPro70-FMWin, 70ProPred, and iPromoter-2L) offered high predictive power. Of these tools, iPro70-FMWin exhibited the best results for most of the metrics used. We present here some potentials and limitations of available tools, and we hope that future work can build upon our effort to systematically characterize this useful class of bioinformatics tools. IMPORTANCE The correct mapping of promoter elements is a crucial step in microbial genomics. Also, when combining new DNA elements into synthetic sequences, predicting the potential generation of new promoter sequences is critical. Over the last years, many bioinformatics tools have been created to allow users to predict promoter elements in a sequence or genome of interest. Here, we assess the predictive power of some of the main prediction tools available using well-defined promoter data sets. Using Escherichia coli as a model organism, we demonstrated that while some tools are biased toward AT-rich sequences, others are very efficient in identifying real promoters with low false-negative rates. We hope the potentials and limitations presented here will help the microbiology community to choose promoter prediction tools among many available alternatives.https://journals.asm.org/doi/10.1128/mSystems.00439-20promoter predictionbacterial promoterscis-regulatory elementsbioinformaticspromoter prediction |
| spellingShingle | Murilo Henrique Anzolini Cassiano Rafael Silva-Rocha Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations mSystems promoter prediction bacterial promoters cis-regulatory elements bioinformatics promoter prediction |
| title | Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations |
| title_full | Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations |
| title_fullStr | Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations |
| title_full_unstemmed | Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations |
| title_short | Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations |
| title_sort | benchmarking bacterial promoter prediction tools potentialities and limitations |
| topic | promoter prediction bacterial promoters cis-regulatory elements bioinformatics promoter prediction |
| url | https://journals.asm.org/doi/10.1128/mSystems.00439-20 |
| work_keys_str_mv | AT murilohenriqueanzolinicassiano benchmarkingbacterialpromoterpredictiontoolspotentialitiesandlimitations AT rafaelsilvarocha benchmarkingbacterialpromoterpredictiontoolspotentialitiesandlimitations |