{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:35:14Z","timestamp":1773275714801,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2685,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Promoter 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.<\/jats:p>\n               <jats:p>Results: We 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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0yves.vandepeer@psb.ugent.be<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp191","type":"journal-article","created":{"date-parts":[[2009,5,28]],"date-time":"2009-05-28T15:48:54Z","timestamp":1243525734000},"page":"i313-i320","source":"Crossref","is-referenced-by-count":59,"title":["Toward a gold standard for promoter prediction evaluation"],"prefix":"10.1093","volume":"25","author":[{"given":"Thomas","family":"Abeel","sequence":"first","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"}]},{"given":"Yvan","family":"Saeys","sequence":"additional","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2009,5,27]]},"reference":[{"key":"2023013112004267600_B1","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1101\/gr.6991408","article-title":"Generic eukaryotic core promoter prediction using structural features of DNA","volume":"18","author":"Abeel","year":"2008","journal-title":"Genome Res."},{"key":"2023013112004267600_B2","doi-asserted-by":"crossref","first-page":"i24","DOI":"10.1093\/bioinformatics\/btn172","article-title":"ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles","volume":"24","author":"Abeel","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112004267600_B3","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/S0076-6879(03)70021-4","article-title":"Computational detection of vertebrate RNA polymerase II promoters","volume":"370","author":"Bajic","year":"2003","journal-title":"Methods Enzymol."},{"key":"2023013112004267600_B4","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1093\/bioinformatics\/18.1.198","article-title":"Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters","volume":"18","author":"Bajic","year":"2002","journal-title":"Bioinformatics"},{"key":"2023013112004267600_B5","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1038\/nbt1032","article-title":"Promoter prediction analysis on the whole human genome","volume":"22","author":"Bajic","year":"2004","journal-title":"Nat. Biotechnol."},{"issue":"Suppl 1","key":"2023013112004267600_B6","doi-asserted-by":"crossref","first-page":"S3.1","DOI":"10.1186\/gb-2006-7-s1-s3","article-title":"Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment","volume":"7","author":"Bajic","year":"2006","journal-title":"Genome Biol."},{"key":"2023013112004267600_B7","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/ng1789","article-title":"Genome-wide analysis of mammalian promoter architecture and evolution","volume":"38","author":"Carninci","year":"2006","journal-title":"Nat. Genet."},{"key":"2023013112004267600_B8","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1038\/ng780","article-title":"Computational identification of promoters and first exons in the human genome","volume":"29","author":"Davuluri","year":"2001","journal-title":"Nat. Genet."},{"key":"2023013112004267600_B9","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1101\/gr.216102","article-title":"Computational detection and location of transcription start sites in mammalian genomic DNA","volume":"12","author":"Down","year":"2002","journal-title":"Genome Res."},{"key":"2023013112004267600_B10","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1101\/gr.7.9.861","article-title":"Eukaryotic promoter recognition","volume":"7","author":"Fickett","year":"1997","journal-title":"Genome Res."},{"key":"2023013112004267600_B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.6831208","article-title":"A code for transcription initiation in mammalian genomes","volume":"18","author":"Frith","year":"2008","journal-title":"Genome Res."},{"key":"2023013112004267600_B12","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1089\/cmb.2006.13.379","article-title":"Using multiple alignments to improve gene prediction","volume":"13","author":"Gross","year":"2006","journal-title":"J. Comput. Biol."},{"key":"2023013112004267600_B13","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1186\/1471-2105-7-446","article-title":"CpGcluster: a distance-based algorithm for CpG-island detection","volume":"7","author":"Hackenberg","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013112004267600_B14","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1093\/bioinformatics\/15.5.356","article-title":"Promoter2.0: for the recognition of PolII promoter sequences","volume":"15","author":"Knudsen","year":"1999","journal-title":"Bioinformatics"},{"key":"2023013112004267600_B15","first-page":"380","article-title":"Stochastic segment models of eukaryotic promoter regions","volume":"1","author":"Ohler","year":"2000","journal-title":"Pac. Symp. Biocomput."},{"key":"2023013112004267600_B16","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1093\/bioinformatics\/18.4.631","article-title":"CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences","volume":"18","author":"Ponger","year":"2002","journal-title":"Bioinformatics"},{"key":"2023013112004267600_B17","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1006\/jmbi.1995.0349","article-title":"Predicting Pol II promoter sequences using transcription factor binding sites","volume":"249","author":"Prestridge","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2023013112004267600_B18","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/S0097-8485(01)00099-7","article-title":"Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome","volume":"26","author":"Reese","year":"2001","journal-title":"Comput. Chem."},{"key":"2023013112004267600_B19","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1038\/nrg2026","article-title":"Mammalian RNA polymerase II core promoters: insights from genome-wide studies","volume":"8","author":"Sandelin","year":"2007","journal-title":"Nat. Rev. Genet."},{"key":"2023013112004267600_B20","doi-asserted-by":"crossref","first-page":"15776","DOI":"10.1073\/pnas.2136655100","article-title":"Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage","volume":"100","author":"Shiraki","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013112004267600_B21","doi-asserted-by":"crossref","first-page":"e472","DOI":"10.1093\/bioinformatics\/btl250","article-title":"ARTS: accurate recognition of transcription starts in human","volume":"22","author":"Sonnenburg","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112004267600_B22","doi-asserted-by":"crossref","first-page":"D97","DOI":"10.1093\/nar\/gkm901","article-title":"Dbtss: database of transcription start sites, progress report 2008","volume":"36","author":"Wakaguri","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112004267600_B23","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.bbrc.2006.06.062","article-title":"A mammalian promoter model links cis elements to genetic networks","volume":"347","author":"Wang","year":"2006","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2023013112004267600_B24","doi-asserted-by":"crossref","first-page":"041908","DOI":"10.1103\/PhysRevE.75.041908","article-title":"Eukaryotic promoter prediction based on relative entropy and positional information","volume":"75","author":"Wu","year":"2007","journal-title":"Phys. Rev. E Stat. Nonlin. Soft Matter Phys."},{"key":"2023013112004267600_B25","doi-asserted-by":"crossref","first-page":"2722","DOI":"10.1093\/bioinformatics\/btl482","article-title":"PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm","volume":"22","author":"Xie","year":"2006","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/12\/i313\/48991115\/bioinformatics_25_12_i313.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/12\/i313\/48991115\/bioinformatics_25_12_i313.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:07:55Z","timestamp":1675199275000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/12\/i313\/187480"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,5,27]]},"references-count":25,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2009,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp191","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,6,15]]},"published":{"date-parts":[[2009,5,27]]}}}