{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:35:01Z","timestamp":1740144901959,"version":"3.37.3"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"3-4","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":5639,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["30470984"],"award-info":[{"award-number":["30470984"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Predicting protein-coding genes still remains a significant challenge. Although a variety of computational programs that use commonly machine learning methods have emerged, the accuracy of predictions remains a low level when implementing in large genomic sequences. Moreover, computational gene finding in newly sequenced genomes is especially a difficult task due to the absence of a training set of abundant validated genes. Here we present a new gene-finding program, SCGPred, to improve the accuracy of prediction by combining multiple sources of evidence. SCGPred can perform both supervised method in previously well-studied genomes and unsupervised one in novel genomes. By testing with datasets composed of large DNA sequences from human and a novel genome of Ustilago maydi, SCGPred gains a significant improvement in comparison to the popular ab initio gene predictors. We also demonstrate that SCGPred can significantly improve prediction in novel genomes by combining several foreign gene finders with similarity alignments, which is superior to other unsupervised methods. Therefore, SCGPred can serve as an alternative gene-finding tool for newly sequenced eukaryotic genomes. The program is freely available at http:\/\/bio.scu.edu.cn\/SCGPred\/.<\/jats:p>","DOI":"10.1016\/s1672-0229(09)60005-x","type":"journal-article","created":{"date-parts":[[2009,3,30]],"date-time":"2009-03-30T20:43:59Z","timestamp":1238445839000},"page":"175-185","source":"Crossref","is-referenced-by-count":5,"title":["SCGPred: A Score-Based Method for Gene Structure Prediction by Combining Multiple Sources of Evidence"],"prefix":"10.1093","volume":"6","author":[{"given":"Xiao","family":"Li","sequence":"first","affiliation":[{"name":"College of Life Sciences, Sichuan University , Chengdu, 610064 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingan","family":"Ren","sequence":"additional","affiliation":[{"name":"College of Mathematics, Sichuan University , Chengdu, 610064 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Weng","sequence":"additional","affiliation":[{"name":"College of Mathematics, Sichuan University , Chengdu, 610064 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoyang","family":"Cai","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Sichuan University , Chengdu, 610064 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunmin","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Mathematics, Sichuan University , Chengdu, 610064 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yizheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Sichuan University , Chengdu, 610064 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,3,27]]},"reference":[{"key":"2024051008244845100_bib1","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1101\/gr.122800","article-title":"An assessment of gene prediction accuracy in large DNA sequences","volume":"10","author":"Guig\u00f3","year":"2000","journal-title":"Genome Res."},{"key":"2024051008244845100_bib2","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1101\/gr.147901","article-title":"Evaluation of gene-finding programs on mammalian sequences","volume":"11","author":"Rogic","year":"2001","journal-title":"Genome Res."},{"key":"2024051008244845100_bib3","doi-asserted-by":"crossref","first-page":"4103","DOI":"10.1093\/nar\/gkf543","article-title":"Current methods of gene prediction, their strengths and weaknesses","volume":"30","author":"Math\u00e9","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2024051008244845100_bib4","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1101\/gr.175701","article-title":"Computational inference of homologous gene structures in the human genome","volume":"11","author":"Yeh","year":"2001","journal-title":"Genome Res."},{"key":"2024051008244845100_bib5","doi-asserted-by":"crossref","first-page":"S140","DOI":"10.1093\/bioinformatics\/17.suppl_1.S140","article-title":"Integrating genomic homology into gene structure prediction","volume":"17","author":"Korf","year":"2001","journal-title":"Bioinformatics"},{"key":"2024051008244845100_bib6","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1101\/gr.871403","article-title":"Comparative gene prediction in human and mouse","volume":"13","author":"Parra","year":"2003","journal-title":"Genome Res."},{"key":"2024051008244845100_bib7","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1101\/gr.10.4.516","article-title":"Ab initio gene finding in Drosophila genomic DNA","volume":"10","author":"Salamov","year":"2000","journal-title":"Genome Res."},{"key":"2024051008244845100_bib8","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/1471-2105-7-62","article-title":"Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources","volume":"7","author":"Stanke","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2024051008244845100_bib9","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","article-title":"Prediction of complete gene structures in human genomic DNA","volume":"268","author":"Burge","year":"1997","journal-title":"J. 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