ArticleBioinformatics (Oxford, England)2009
Toward a gold standard for promoter prediction evaluation.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Predicting Promoters in Multiple Prokaryotes with Prompt.Interdisciplinary sciences, computational life sciences · 2024Article
- DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.GigaScience · 2024Article
- Explainable artificial intelligence as a reliable annotator of archaeal promoter regions.Scientific reports · 2023Article
- Deep learning and support vector machines for transcription start site identification.PeerJ. Computer science · 2023Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes.Briefings in bioinformatics · 2021Article
- DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.Bioinformatics (Oxford, England) · 2021Article
- Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy.Scientific reports · 2018Article
- TSSPlant: a new tool for prediction of plant Pol II promoters.Nucleic acids research · 2017Article
- TIPR: transcription initiation pattern recognition on a genome scale.Bioinformatics (Oxford, England) · 2015Article
- SVM2Motif--Reconstructing Overlapping DNA Sequence Motifs by Mimicking an SVM Predictor.PloS one · 2015Article
- The impact of sequence length and number of sequences on promoter prediction performance.BMC bioinformatics · 2015Article
- Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci.Journal of immunology (Baltimore, Md. : 1950) · 2014Article
- Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis.The Plant cell · 2014Article
- NPEST: a nonparametric method and a database for transcription start site prediction.Quantitative biology (Beijing, China) · 2013Article
- Integrative annotation of chromatin elements from ENCODE data.Nucleic acids research · 2013Article
- CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes.BMC genomics · 2012Article
- ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites.Bioinformatics (Oxford, England) · 2012Article
- A comparison study on feature selection of DNA structural properties for promoter prediction.BMC bioinformatics · 2012Article
- The regulatory epicenter of miRNAs.Journal of biosciences · 2011Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationPromoter prediction is an important task in genome annotation projects, and during the past years many new promoter prediction programs (PPPs) have emerged. However, many of these programs are compared inadequately to other programs. In most cases, only a small portion of the genome is used to evaluate the program, which is not a realistic setting for whole genome annotation projects. In addition, a common evaluation design to properly compare PPPs is still lacking.
resultsWe present a large-scale benchmarking study of 17 state-of-the-art PPPs. A multi-faceted evaluation strategy is proposed that can be used as a gold standard for promoter prediction evaluation, allowing authors of promoter prediction software to compare their method to existing methods in a proper way. This evaluation strategy is subsequently used to compare the chosen promoter predictors, and an in-depth analysis on predictive performance, promoter class specificity, overlap between predictors and positional bias of the predictions is conducted. AVAILABILITY: We provide the implementations of the four protocols, as well as the datasets required to perform the benchmarks to the academic community free of charge on request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.