{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T11:12:51Z","timestamp":1675336371305},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Many problems in genome annotation are tackled by using a classification model to predict functional sites such as splice sites, translation start sites or stop codons. Locating the correct position of these sites remains one of the most important but also one of the most difficult issues in the structural annotation of genomes. Most of the software currently in use is written for a very specific problem, thereby limiting the possibilities for reuse.<\/jats:p>\n               <jats:p>Summary: We developed a software platform that uses a very general approach towards the classification of functional sites in DNA sequences. The program uses an ab initio approach towards the identification of these sites, and extends SpliceMachine, a previously developed splice site predictor that shows state-of-the-art performance for both donor and acceptor splice site recognition in the human and Arabidopsis thaliana genome.<\/jats:p>\n               <jats:p>Availability: The program is developed as a stand-alone Java application, and is available as GPLv3 open-source software. The program, source and documentation can be obtained from the \u2018Software\u2019 section at http:\/\/bioinformatics.psb.ugent.be\/<\/jats:p>\n               <jats:p>Contact: \u00a0Yves.VandePeer@psb.ugent.be<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn225","type":"journal-article","created":{"date-parts":[[2008,5,13]],"date-time":"2008-05-13T00:13:13Z","timestamp":1210637593000},"page":"1532-1533","source":"Crossref","is-referenced-by-count":0,"title":["FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA"],"prefix":"10.1093","volume":"24","author":[{"given":"Michiel","family":"Van Bel","sequence":"first","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yvan","family":"Saeys","sequence":"additional","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB and 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,5,12]]},"reference":[{"key":"2023020210351234900_B1","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.1093\/bioinformatics\/bti166","article-title":"Predicting splice sites from high-dimensional local context representations","volume":"21","author":"Degroeve","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020210351234900_B2","volume-title":"Pro Apache log4j","author":"Gupta","year":"2005","edition":"2nd edn"},{"key":"2023020210351234900_B3","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/3-540-45727-5_10","article-title":"EuG\u00e8ne, an eukaryotic gene finder that combines several types of evidence","volume":"Vol. 2066","author":"Schiex","year":"2001","journal-title":"Lect. 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