{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,13]],"date-time":"2024-09-13T17:10:18Z","timestamp":1726247418894},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/1471-2105-5-40","type":"journal-article","created":{"date-parts":[[2004,4,22]],"date-time":"2004-04-22T06:22:34Z","timestamp":1082614954000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["Pegasys: software for executing and integrating analyses of biological sequences"],"prefix":"10.1186","volume":"5","author":[{"given":"Sohrab P","family":"Shah","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David YM","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica N","family":"Sawkins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey C","family":"Druce","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerald","family":"Quon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Drew","family":"Lett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grace XY","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tao","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"BF Francis","family":"Ouellette","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2004,4,19]]},"reference":[{"key":"156_CR1","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1093\/nar\/30.1.38","volume":"30","author":"T Hubbard","year":"2002","unstructured":"Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M: The Ensembl genome database project.\n                           Nucleic Acids Res 2002, 30: 38\u201341. 10.1093\/nar\/30.1.38","journal-title":"Nucleic Acids Res"},{"key":"156_CR2","volume-title":"An integrated computational pipeline and database to support whole-genome sequence annotation","author":"CJ Mungall","year":"2002","unstructured":"Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, Lewis SE: An integrated computational pipeline and database to support whole-genome sequence annotation.\n                           Genome Biol 2002., 3(12): RESEARCH0081. Epub 2002 Dec 23. Review"},{"issue":"8","key":"156_CR3","doi-asserted-by":"publisher","first-page":"2187","DOI":"10.1093\/nar\/gkg312","volume":"31","author":"F Meyer","year":"2003","unstructured":"Meyer F, Goesmann A, McHardy A, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, P\u00fchler A: GenDB \u2013 an open source genome annotation system for prokaryote genomes.\n                           Nucleic Acids Res 2003, 31(8):2187\u20132195. 10.1093\/nar\/gkg312","journal-title":"Nucleic Acids Res"},{"key":"156_CR4","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1093\/nar\/gkg059","volume":"31","author":"Q Yuan","year":"2003","unstructured":"Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell C: The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.\n                           Nucleic Acids Res 2003, 31: 229\u2013233. 10.1093\/nar\/gkg059","journal-title":"Nucleic Acids Res"},{"key":"156_CR5","doi-asserted-by":"publisher","first-page":"S140","DOI":"10.1093\/bioinformatics\/17.suppl_1.S140","volume":"17","author":"I Korf","year":"2001","unstructured":"Korf I, Flicek P, Duan D, Brent MR: Integrating genomic homology into gene structure prediction.\n                           Bioinformatics 2001, 17: S140-S148. Suppl 1","journal-title":"Bioinformatics"},{"issue":"3","key":"156_CR6","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1016\/S0168-1656(00)00196-6","volume":"78","author":"C Math\u00e9","year":"2000","unstructured":"Math\u00e9 C, D\u00e9hais P, Pavy N, Rombauts S, Van Montagu M, Rouz\u00e9 P: Gene prediction and gene classes in Arabidopsis thaliana.\n                           J Biotechnol 2000, 78(3):293\u2013299. 10.1016\/S0168-1656(00)00196-6","journal-title":"J Biotechnol"},{"issue":"5","key":"156_CR7","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1101\/gr.175701","volume":"11","author":"R Yeh","year":"2001","unstructured":"Yeh R, Lim L, Burge C: Computational inference of homologous gene structures in the human genome.\n                           Genome Res 2001, 11(5):803\u2013816. 10.1101\/gr.175701","journal-title":"Genome Res"},{"issue":"8","key":"156_CR8","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1093\/bioinformatics\/18.8.1034","volume":"18","author":"S Rogic","year":"2002","unstructured":"Rogic S, Ouellette B, Mackworth A: Improving gene recognition accuracy by combining predictions from two gene-finding programs.\n                           Bioinformatics 2002, 18(8):1034\u20131045. 10.1093\/bioinformatics\/18.8.1034","journal-title":"Bioinformatics"},{"key":"156_CR9","unstructured":"General Feature Format[http:\/\/www.sanger.ac.uk\/Software\/formats\/GFF\/index.shtml]"},{"key":"156_CR10","unstructured":"GAME XML DTD[http:\/\/flybase.bio.indiana.edu\/annot\/gamexml.dtd.txt]"},{"key":"156_CR11","volume-title":"Apollo: a sequence annotation editor","author":"SE Lewis","year":"2002","unstructured":"Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME: Apollo: a sequence annotation editor.\n                           Genome Biol 2002., 3(12): RESEARCH0082. Epub 2002 Dec 23. Review."},{"issue":"3","key":"156_CR12","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"S Altschul","year":"1990","unstructured":"Altschul S, Gish W, Miller W, Myers E, Lipman D: Basic local alignment search tool.\n                           J Mol Biol 1990, 215(3):403\u2013410. 10.1006\/jmbi.1990.9999","journal-title":"J Mol Biol"},{"issue":"17","key":"156_CR13","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"S Altschul","year":"1997","unstructured":"Altschul S, Madden T, Sch\u00e4ffer A, Zhang J, Zhang Z, Miller W, Lipman D: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.\n                           Nucleic Acids Res 1997, 25(17):3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"key":"156_CR14","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-2-7","volume":"2","author":"R Dowell","year":"2001","unstructured":"Dowell R, Jokerst R, Day A, Eddy S, Stein L: The distributed annotation system.\n                           BMC Bioinformatics 2001, 2: 7\u20137. 10.1186\/1471-2105-2-7","journal-title":"BMC Bioinformatics"},{"key":"156_CR15","volume-title":"R Foundation for Statistical Computing, Vienna, Austria","author":"R Development Core Team","year":"2003","unstructured":"R Development Core Team: R: A language and environment for statistical computing.\n                           R Foundation for Statistical Computing, Vienna, Austria 2003. [ISBN 3\u2013900051\u201300\u20133] [http:\/\/www.R-project.org]"},{"issue":"11","key":"156_CR16","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1093\/bioinformatics\/16.11.1040","volume":"16","author":"J Bedell","year":"2000","unstructured":"Bedell J, Korf I, Gish W: Masker Aid: a performance enhancement to RepeatMasker.\n                           Bioinformatics 2000, 16(11):1040\u20131041. 10.1093\/bioinformatics\/16.11.1040","journal-title":"Bioinformatics"},{"key":"156_CR17","unstructured":"Gish W: WU BLAST 2.0.[http:\/\/blast.wustl.edu\/blast\/README.html]"},{"issue":"6","key":"156_CR18","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite.\n                           Trends Genet 2000, 16(6):276\u2013277. 10.1016\/S0168-9525(00)02024-2","journal-title":"Trends Genet"},{"key":"156_CR19","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"T Smith","year":"1981","unstructured":"Smith T, Waterman M: Identification of common molecular subsequences.\n                           J Mol Biol 1981, 147: 195\u2013197.","journal-title":"J Mol Biol"},{"key":"156_CR20","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","volume":"268","author":"C Burge","year":"1997","unstructured":"Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA.\n                           J Mol Biol 1997, 268: 78\u201394. 10.1006\/jmbi.1997.0951","journal-title":"J Mol Biol"},{"key":"156_CR21","first-page":"179","volume":"5","author":"A Krogh","year":"1997","unstructured":"Krogh A: Two methods for improving performance of an HMM and their application for gene finding.\n                           Proc Int Conf Intell Syst Mol Biol 1997, 5: 179\u2013186.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"issue":"4","key":"156_CR22","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1101\/gr.926603","volume":"13","author":"M Brudno","year":"2003","unstructured":"Brudno M, Do C, Cooper G, Kim M, Davydov E, Green E, Sidow A, Batzoglou S: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.\n                           Genome Res 2003, 13(4):721\u2013731. 10.1101\/gr.926603","journal-title":"Genome Res"},{"issue":"9","key":"156_CR23","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1101\/gr.8.9.967","volume":"8","author":"L Florea","year":"1998","unstructured":"Florea L, Hartzell G, Zhang Z, Rubin G, Miller W: A computer program for aligning a cDNA sequence with a genomic DNA sequence.\n                           Genome Res 1998, 8(9):967\u2013974.","journal-title":"Genome Res"},{"issue":"5","key":"156_CR24","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","volume":"25","author":"T Lowe","year":"1997","unstructured":"Lowe T, Eddy S: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.\n                           Nucleic Acids Res 1997, 25(5):955\u2013964. 10.1093\/nar\/25.5.955","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"156_CR25","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1093\/nar\/29.5.1185","volume":"29","author":"M Pertea","year":"2001","unstructured":"Pertea M, Lin X, Salzberg S: GeneSplicer: a new computational method for splice site prediction.\n                           Nucleic Acids Res 2001, 29(5):1185\u20131190. 10.1093\/nar\/29.5.1185","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"156_CR26","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1101\/gr.403602","volume":"12","author":"L Stein","year":"2002","unstructured":"Stein L, Mungall C, Shu S, Gaudy M, Mangone M, Day A, Nickerson E, Stajich J, Harris T, Arva A, Lewis S: The generic genome browser: a building block for a model organism system database.\n                           Genome Res 2002, 12(10):1599\u20131610. 10.1101\/gr.403602","journal-title":"Genome Res"},{"key":"156_CR27","unstructured":"OpenPBS[http:\/\/www.openpbs.org]"},{"key":"156_CR28","volume-title":"Object-oriented Analysis and Design with Applications","author":"G Booch","year":"1994","unstructured":"Booch G: Object-oriented Analysis and Design with Applications The Benjamin\/Cummings Publishing Company 1994."},{"key":"156_CR29","unstructured":"Ensj[http:\/\/www.ensembl.org\/java\/]"},{"key":"156_CR30","unstructured":"BioJava.org[http:\/\/www.biojava.org]"},{"issue":"8","key":"156_CR31","doi-asserted-by":"crossref","first-page":"1904","DOI":"10.1101\/gr.1363103","volume":"13","author":"S Hoon","year":"2003","unstructured":"Hoon S, Ratnapu K, Chia J, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, Stupka E: Biopipe: a flexible framework for protocol-based bioinformatics analysis.\n                           Genome Res 2003, 13(8):1904\u20131915.","journal-title":"Genome Res"},{"key":"156_CR32","unstructured":"Trolltech \u2013 Qt Overview[http:\/\/www.trolltech.com\/products\/qt\/index.html]"},{"issue":"Suppl 1","key":"156_CR33","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1093\/bioinformatics\/btg1031","volume":"19","author":"A Rowe","year":"2003","unstructured":"Rowe A, Kalaitzopoulos D, Osmond M, Ghanem M, Guo Y: The discovery net system for high throughput bioinformatics.\n                           Bioinformatics 2003, 19(Suppl 1):225\u2013225. 10.1093\/bioinformatics\/btg1031","journal-title":"Bioinformatics"},{"key":"156_CR34","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1093\/nar\/gkg006","volume":"31","author":"S Griffiths-Jones","year":"2003","unstructured":"Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy S: Rfam: an RNA family database.\n                           Nucleic Acids Res 2003, 31: 439\u2013441. 10.1093\/nar\/gkg006","journal-title":"Nucleic Acids Res"},{"issue":"23","key":"156_CR35","doi-asserted-by":"publisher","first-page":"4636","DOI":"10.1093\/nar\/27.23.4636","volume":"27","author":"A Delcher","year":"1999","unstructured":"Delcher A, Harmon D, Kasif S, White O, Salzberg S: Improved microbial gene identification with GLIMMER.\n                           Nucleic Acids Res 1999, 27(23):4636\u20134641. 10.1093\/nar\/27.23.4636","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"156_CR36","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1093\/nar\/26.2.544","volume":"26","author":"S Salzberg","year":"1998","unstructured":"Salzberg S, Delcher A, Kasif S, White O: Microbial gene identification using interpolated Markov models.\n                           Nucleic Acids Res 1998, 26(2):544\u2013548. 10.1093\/nar\/26.2.544","journal-title":"Nucleic Acids Res"},{"key":"156_CR37","first-page":"111","volume-title":"In JOBIM","author":"T Schiex","year":"2000","unstructured":"Schiex T, A M, P R: EUGENE: An Eukaryotic Gene Finder That Combines Several Sources of Evidence.\n                           In JOBIM 2000, 111\u2013125."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-40.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,13]],"date-time":"2024-09-13T16:03:28Z","timestamp":1726243408000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-5-40"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,4,19]]},"references-count":37,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2004,12]]}},"alternative-id":["156"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-5-40","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2004,4,19]]},"assertion":[{"value":"27 February 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 April 2004","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 April 2004","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"40"}}