{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T01:30:39Z","timestamp":1772069439490,"version":"3.50.1"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,5,3]],"date-time":"2012-05-03T00:00:00Z","timestamp":1336003200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Res Notes"],"published-print":{"date-parts":[[2012,12]]},"DOI":"10.1186\/1756-0500-5-213","type":"journal-article","created":{"date-parts":[[2012,5,3]],"date-time":"2012-05-03T06:16:41Z","timestamp":1336025801000},"source":"Crossref","is-referenced-by-count":140,"title":["Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences"],"prefix":"10.1186","volume":"5","author":[{"given":"J\u00e9r\u00f4me","family":"Grimplet","sequence":"first","affiliation":[]},{"given":"John","family":"Van Hemert","sequence":"additional","affiliation":[]},{"given":"Pablo","family":"Carbonell-Bejerano","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9","family":"D\u00edaz-Riquelme","sequence":"additional","affiliation":[]},{"given":"Julie","family":"Dickerson","sequence":"additional","affiliation":[]},{"given":"Anne","family":"Fennell","sequence":"additional","affiliation":[]},{"given":"Mario","family":"Pezzotti","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 M","family":"Mart\u00ednez-Zapater","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,5,3]]},"reference":[{"key":"1563_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1201\/b10948-2","volume-title":"Genetics, Genomics, and Breeding of Grapes","author":"A Bouquet","year":"2011","unstructured":"Bouquet A: Grapevines and Viticulture. Genetics, Genomics, and Breeding of Grapes. Edited by: Adam-Blondon A-F, Martinez-Zapater JM, Kole C. 2011, Science Publishers, Enfield, 1-29."},{"issue":"9","key":"1563_CR2","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","volume":"19","author":"M Krzywinski","year":"2009","unstructured":"Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19 (9): 1639-1645. 10.1101\/gr.092759.109.","journal-title":"Genome Res"},{"key":"1563_CR3","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1201\/b10948-10","volume-title":"Genetics, Genomics, and Breeding of Grapes","author":"AF Adam-Blondon","year":"2011","unstructured":"Adam-Blondon AF, Jaillon O, Vezzulli S, Zharkikh A, Troggio M, Velasco R: Genome Sequence Initiatives. Genetics, Genomics, and Breeding of Grapes. Edited by: Adam-Blondon A-F, Martinez-Zapater JM, Kole C. 2011, Science Publishers, Enfield, 211-234."},{"key":"1563_CR4","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1201\/b10948-11","volume-title":"Genetics, Genomics, and Breeding of Grapes","author":"R Tillett","year":"2011","unstructured":"Tillett R, Cushman J: Vitis Functional Genomics: Open Systems for Transcriptome Analysis. Genetics, Genomics, and Breeding of Grapes. Edited by: Adam-Blondon A-F, Martinez-Zapater JM, Kole C. 2011, Science Publishers, Enfield, 235-269."},{"key":"1563_CR5","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1201\/b10948-12","volume-title":"Genetics, Genomics, and Breeding of Grapes","author":"C Romieu","year":"2011","unstructured":"Romieu C, Kappel C, Delrot S: Functional Genomics: Closed System Approaches for Transcriptome Analyses. Genetics, Genomics, and Breeding of Grapes. Edited by: Adam-Blondon A-F, Martinez-Zapater JM, Kole C. 2011, Science Publishers, Enfield, 270-298."},{"key":"1563_CR6","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1201\/b10948-13","volume-title":"Genetics, Genomics, and Breeding of Grapes","author":"S Lund","year":"2011","unstructured":"Lund S, Cramer G: Functional Genomics: Proteomics and Metabolomics. Genetics, Genomics, and Breeding of Grapes. Edited by: Adam-Blondon A-F, Martinez-Zapater JM, Kole C. 2011, Science Publishers, Enfield, 299-316."},{"key":"1563_CR7","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1201\/b10948-14","volume-title":"Genetics, Genomics, and Breeding of Grapes","author":"J Grimplet","year":"2011","unstructured":"Grimplet J, Dickerson J, Adam-Blondon A-F, Cramer G: Bioinformatics Tools in Grapevine Genomics. Genetics, Genomics, and Breeding of Grapes. Edited by: Adam-Blondon A-F, Martinez-Zapater JM, Kole C. 2011, Science Publishers, Enfield, 317-331."},{"issue":"12","key":"1563_CR8","doi-asserted-by":"publisher","first-page":"e1326","DOI":"10.1371\/journal.pone.0001326","volume":"2","author":"R Velasco","year":"2007","unstructured":"Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, et al: A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE. 2007, 2 (12): e1326-10.1371\/journal.pone.0001326.","journal-title":"PLoS ONE"},{"issue":"7161","key":"1563_CR9","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1038\/nature06148","volume":"449","author":"O Jaillon","year":"2007","unstructured":"Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007, 449 (7161): 463-467. 10.1038\/nature06148.","journal-title":"Nature"},{"issue":"9","key":"1563_CR10","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.1101\/gr.149502","volume":"12","author":"KL Howe","year":"2002","unstructured":"Howe KL, Chothia T, Durbin R: GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res. 2002, 12 (9): 1418-1427. 10.1101\/gr.149502.","journal-title":"Genome Res"},{"issue":"18","key":"1563_CR11","doi-asserted-by":"publisher","first-page":"3596","DOI":"10.1093\/bioinformatics\/bti609","volume":"21","author":"JE Allen","year":"2005","unstructured":"Allen JE, Salzberg SL: JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics. 2005, 21 (18): 3596-3603. 10.1093\/bioinformatics\/bti609.","journal-title":"Bioinformatics"},{"key":"1563_CR12","volume-title":"Universita\u2019 Degli Studi Di Padova","author":"C Forcato","year":"2010","unstructured":"Forcato C: Gene prediction and functional annotation in the Vitis vinifera genome. Universita\u2019 Degli Studi Di Padova. 2010, , , PhD Thesis"},{"issue":"2","key":"1563_CR13","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/s10142-006-0039-y","volume":"7","author":"G Cramer","year":"2007","unstructured":"Cramer G, Ergul A, Grimplet J, Tillett R, Tattersall E, Bohlman M, Vincent D, Sonderegger J, Evans J, Osborne C, et al: Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics. 2007, 7 (2): 111-134. 10.1007\/s10142-006-0039-y.","journal-title":"Funct Integr Genomics"},{"key":"1563_CR14","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1186\/1471-2229-10-224","volume":"10","author":"MA Pontin","year":"2010","unstructured":"Pontin MA, Piccoli PN, Francisco R, Bottini R, Martinez-Zapater JM, Lijavetzky D: Transcriptome changes in grapevine (Vitis vinifera L.) cv. Malbec leaves induced by ultraviolet-B radiation. BMC Plant Biol. 2010, 10: 224-10.1186\/1471-2229-10-224.","journal-title":"BMC Plant Biol"},{"issue":"12","key":"1563_CR15","doi-asserted-by":"publisher","first-page":"e8365","DOI":"10.1371\/journal.pone.0008365","volume":"4","author":"J Grimplet","year":"2009","unstructured":"Grimplet J, Cramer GR, Dickerson JA, Mathiason K, Van Hemert J, Fennell AY: VitisNet: \u201cOmics\u201d integration through grapevine molecular networks. PLoS ONE. 2009, 4 (12): e8365-10.1371\/journal.pone.0008365.","journal-title":"PLoS ONE"},{"issue":"1","key":"1563_CR16","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1101\/gr.828403","volume":"13","author":"DB Jaffe","year":"2003","unstructured":"Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES: Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 2003, 13 (1): 91-96. 10.1101\/gr.828403.","journal-title":"Genome Res"},{"key":"1563_CR17","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1186\/1471-2164-11-459","volume":"11","author":"MV Sharakhova","year":"2010","unstructured":"Sharakhova MV, George P, Brusentsova IV, Leman SC, Bailey JA, Smith CD, Sharakhov IV: Genome mapping and characterization of the Anopheles gambiae heterochromatin. BMC Genomics. 2010, 11: 459-10.1186\/1471-2164-11-459.","journal-title":"BMC Genomics"},{"issue":"5","key":"1563_CR18","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1093\/jhered\/esm027","volume":"98","author":"T Derrien","year":"2007","unstructured":"Derrien T, Andre C, Galibert F, Hitte C: Analysis of the unassembled part of the dog genome sequence: chromosomal localization of 115 genes inferred from multispecies comparative genomics. J Hered. 2007, 98 (5): 461-467. 10.1093\/jhered\/esm027.","journal-title":"J Hered"},{"issue":"suppl_1","key":"1563_CR19","first-page":"D966","volume":"36","author":"AY Guo","year":"2008","unstructured":"Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J: PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res. 2008, 36 (suppl_1): D966-D969.","journal-title":"Nucleic Acids Res"},{"key":"1563_CR20","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/1471-2105-8-42","volume":"8","author":"D Riano-Pachon","year":"2007","unstructured":"Riano-Pachon D, Ruzicic S, Dreyer I, Mueller-Roeber B: PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics. 2007, 8: 42-10.1186\/1471-2105-8-42.","journal-title":"BMC Bioinformatics"},{"issue":"1\u20132","key":"1563_CR21","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1089\/10665270050081478","volume":"7","author":"Z Zhang","year":"2000","unstructured":"Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000, 7 (1\u20132): 203-214.","journal-title":"J Comput Biol"},{"issue":"1\u20132","key":"1563_CR22","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.gene.2007.07.016","volume":"402","author":"FY Peng","year":"2007","unstructured":"Peng FY, Reid KE, Liao N, Schlosser J, Lijavetzky D, Holt R, Mart\u00ednez Zapater JM, Jones S, Marra M, Bohlmann J, et al: Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development. Gene. 2007, 402 (1\u20132): 40-50.","journal-title":"Gene"},{"issue":"18","key":"1563_CR23","doi-asserted-by":"publisher","first-page":"5539","DOI":"10.1093\/nar\/gkh894","volume":"32","author":"A Ruepp","year":"2004","unstructured":"Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M, et al: The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004, 32 (18): 5539-5545. 10.1093\/nar\/gkh894.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1563_CR24","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al: Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038\/75556.","journal-title":"Nat Genet"},{"issue":"Database issue","key":"1563_CR25","doi-asserted-by":"publisher","first-page":"D181","DOI":"10.1093\/nar\/gkj001","volume":"34","author":"MH Saier","year":"2006","unstructured":"Saier MH, Tran CV, Barabote RD: TCDB: the transporter classification database for membrane transport protein analyses and information. Nucleic Acids Res. 2006, 34 (Database issue): D181-D186.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Research Notes"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1756-0500-5-213.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1756-0500-5-213\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1756-0500-5-213.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T02:53:32Z","timestamp":1548125612000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcresnotes.biomedcentral.com\/articles\/10.1186\/1756-0500-5-213"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,5,3]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["1563"],"URL":"https:\/\/doi.org\/10.1186\/1756-0500-5-213","relation":{},"ISSN":["1756-0500"],"issn-type":[{"value":"1756-0500","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,5,3]]},"article-number":"213"}}