Literature DB >> 15123596

GeneWise and Genomewise.

Ewan Birney1, Michele Clamp, Richard Durbin.   

Abstract

We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure. Both algorithms are heavily used by the Ensembl annotation system. The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence.

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Year:  2004        PMID： 15123596      PMCID： PMC479130          DOI： 10.1101/gr.1865504

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  26 in total

1.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

2.  Computational inference of homologous gene structures in the human genome.

Authors:  R F Yeh; L P Lim; C B Burge
Journal:  Genome Res       Date:  2001-05       Impact factor: 9.043

3.  Comparative ab initio prediction of gene structures using pair HMMs.

Authors:  Irmtraud M Meyer; Richard Durbin
Journal:  Bioinformatics       Date:  2002-10       Impact factor: 6.937

4.  The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.

Authors:  Paramvir Dehal; Yutaka Satou; Robert K Campbell; Jarrod Chapman; Bernard Degnan; Anthony De Tomaso; Brad Davidson; Anna Di Gregorio; Maarten Gelpke; David M Goodstein; Naoe Harafuji; Kenneth E M Hastings; Isaac Ho; Kohji Hotta; Wayne Huang; Takeshi Kawashima; Patrick Lemaire; Diego Martinez; Ian A Meinertzhagen; Simona Necula; Masaru Nonaka; Nik Putnam; Sam Rash; Hidetoshi Saiga; Masanobu Satake; Astrid Terry; Lixy Yamada; Hong-Gang Wang; Satoko Awazu; Kaoru Azumi; Jeffrey Boore; Margherita Branno; Stephen Chin-Bow; Rosaria DeSantis; Sharon Doyle; Pilar Francino; David N Keys; Shinobu Haga; Hiroko Hayashi; Kyosuke Hino; Kaoru S Imai; Kazuo Inaba; Shungo Kano; Kenji Kobayashi; Mari Kobayashi; Byung-In Lee; Kazuhiro W Makabe; Chitra Manohar; Giorgio Matassi; Monica Medina; Yasuaki Mochizuki; Steve Mount; Tomomi Morishita; Sachiko Miura; Akie Nakayama; Satoko Nishizaka; Hisayo Nomoto; Fumiko Ohta; Kazuko Oishi; Isidore Rigoutsos; Masako Sano; Akane Sasaki; Yasunori Sasakura; Eiichi Shoguchi; Tadasu Shin-i; Antoinetta Spagnuolo; Didier Stainier; Miho M Suzuki; Olivier Tassy; Naohito Takatori; Miki Tokuoka; Kasumi Yagi; Fumiko Yoshizaki; Shuichi Wada; Cindy Zhang; P Douglas Hyatt; Frank Larimer; Chris Detter; Norman Doggett; Tijana Glavina; Trevor Hawkins; Paul Richardson; Susan Lucas; Yuji Kohara; Michael Levine; Nori Satoh; Daniel S Rokhsar
Journal:  Science       Date:  2002-12-13       Impact factor: 47.728

5.  Initial sequencing and comparative analysis of the mouse genome.

Authors:  Robert H Waterston; Kerstin Lindblad-Toh; Ewan Birney; Jane Rogers; Josep F Abril; Pankaj Agarwal; Richa Agarwala; Rachel Ainscough; Marina Alexandersson; Peter An; Stylianos E Antonarakis; John Attwood; Robert Baertsch; Jonathon Bailey; Karen Barlow; Stephan Beck; Eric Berry; Bruce Birren; Toby Bloom; Peer Bork; Marc Botcherby; Nicolas Bray; Michael R Brent; Daniel G Brown; Stephen D Brown; Carol Bult; John Burton; Jonathan Butler; Robert D Campbell; Piero Carninci; Simon Cawley; Francesca Chiaromonte; Asif T Chinwalla; Deanna M Church; Michele Clamp; Christopher Clee; Francis S Collins; Lisa L Cook; Richard R Copley; Alan Coulson; Olivier Couronne; James Cuff; Val Curwen; Tim Cutts; Mark Daly; Robert David; Joy Davies; Kimberly D Delehaunty; Justin Deri; Emmanouil T Dermitzakis; Colin Dewey; Nicholas J Dickens; Mark Diekhans; Sheila Dodge; Inna Dubchak; Diane M Dunn; Sean R Eddy; Laura Elnitski; Richard D Emes; Pallavi Eswara; Eduardo Eyras; Adam Felsenfeld; Ginger A Fewell; Paul Flicek; Karen Foley; Wayne N Frankel; Lucinda A Fulton; Robert S Fulton; Terrence S Furey; Diane Gage; Richard A Gibbs; Gustavo Glusman; Sante Gnerre; Nick Goldman; Leo Goodstadt; Darren Grafham; Tina A Graves; Eric D Green; Simon Gregory; Roderic Guigó; Mark Guyer; Ross C Hardison; David Haussler; Yoshihide Hayashizaki; LaDeana W Hillier; Angela Hinrichs; Wratko Hlavina; Timothy Holzer; Fan Hsu; Axin Hua; Tim Hubbard; Adrienne Hunt; Ian Jackson; David B Jaffe; L Steven Johnson; Matthew Jones; Thomas A Jones; Ann Joy; Michael Kamal; Elinor K Karlsson; Donna Karolchik; Arkadiusz Kasprzyk; Jun Kawai; Evan Keibler; Cristyn Kells; W James Kent; Andrew Kirby; Diana L Kolbe; Ian Korf; Raju S Kucherlapati; Edward J Kulbokas; David Kulp; Tom Landers; J P Leger; Steven Leonard; Ivica Letunic; Rosie Levine; Jia Li; Ming Li; Christine Lloyd; Susan Lucas; Bin Ma; Donna R Maglott; Elaine R Mardis; Lucy Matthews; Evan Mauceli; John H Mayer; Megan McCarthy; W Richard McCombie; Stuart McLaren; Kirsten McLay; John D McPherson; Jim Meldrim; Beverley Meredith; Jill P Mesirov; Webb Miller; Tracie L Miner; Emmanuel Mongin; Kate T Montgomery; Michael Morgan; Richard Mott; James C Mullikin; Donna M Muzny; William E Nash; Joanne O Nelson; Michael N Nhan; Robert Nicol; Zemin Ning; Chad Nusbaum; Michael J O'Connor; Yasushi Okazaki; Karen Oliver; Emma Overton-Larty; Lior Pachter; Genís Parra; Kymberlie H Pepin; Jane Peterson; Pavel Pevzner; Robert Plumb; Craig S Pohl; Alex Poliakov; Tracy C Ponce; Chris P Ponting; Simon Potter; Michael Quail; Alexandre Reymond; Bruce A Roe; Krishna M Roskin; Edward M Rubin; Alistair G Rust; Ralph Santos; Victor Sapojnikov; Brian Schultz; Jörg Schultz; Matthias S Schwartz; Scott Schwartz; Carol Scott; Steven Seaman; Steve Searle; Ted Sharpe; Andrew Sheridan; Ratna Shownkeen; Sarah Sims; Jonathan B Singer; Guy Slater; Arian Smit; Douglas R Smith; Brian Spencer; Arne Stabenau; Nicole Stange-Thomann; Charles Sugnet; Mikita Suyama; Glenn Tesler; Johanna Thompson; David Torrents; Evanne Trevaskis; John Tromp; Catherine Ucla; Abel Ureta-Vidal; Jade P Vinson; Andrew C Von Niederhausern; Claire M Wade; Melanie Wall; Ryan J Weber; Robert B Weiss; Michael C Wendl; Anthony P West; Kris Wetterstrand; Raymond Wheeler; Simon Whelan; Jamey Wierzbowski; David Willey; Sophie Williams; Richard K Wilson; Eitan Winter; Kim C Worley; Dudley Wyman; Shan Yang; Shiaw-Pyng Yang; Evgeny M Zdobnov; Michael C Zody; Eric S Lander
Journal:  Nature       Date:  2002-12-05       Impact factor: 49.962

6.  Gene finding with a hidden Markov model of genome structure and evolution.

Authors:  Jakob Skou Pedersen; Jotun Hein
Journal:  Bioinformatics       Date:  2003-01-22       Impact factor: 6.937

7.  Comparative gene prediction in human and mouse.

Authors:  Genís Parra; Pankaj Agarwal; Josep F Abril; Thomas Wiehe; James W Fickett; Roderic Guigó
Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043

Review 8.  Computational prediction of eukaryotic protein-coding genes.

Authors:  Michael Q Zhang
Journal:  Nat Rev Genet       Date:  2002-09       Impact factor: 53.242

9.  GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.

Authors:  Kevin L Howe; Tom Chothia; Richard Durbin
Journal:  Genome Res       Date:  2002-09       Impact factor: 9.043

10.  Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.

Authors:  Paul Flicek; Evan Keibler; Ping Hu; Ian Korf; Michael R Brent
Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043
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3.  The Ensembl automatic gene annotation system.

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Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

4.  EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches.

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Review 5.  An overview of Ensembl.

Authors:  Ewan Birney; T Daniel Andrews; Paul Bevan; Mario Caccamo; Yuan Chen; Laura Clarke; Guy Coates; James Cuff; Val Curwen; Tim Cutts; Thomas Down; Eduardo Eyras; Xose M Fernandez-Suarez; Paul Gane; Brian Gibbins; James Gilbert; Martin Hammond; Hans-Rudolf Hotz; Vivek Iyer; Kerstin Jekosch; Andreas Kahari; Arek Kasprzyk; Damian Keefe; Stephen Keenan; Heikki Lehvaslaiho; Graham McVicker; Craig Melsopp; Patrick Meidl; Emmanuel Mongin; Roger Pettett; Simon Potter; Glenn Proctor; Mark Rae; Steve Searle; Guy Slater; Damian Smedley; James Smith; Will Spooner; Arne Stabenau; James Stalker; Roy Storey; Abel Ureta-Vidal; K Cara Woodwark; Graham Cameron; Richard Durbin; Anthony Cox; Tim Hubbard; Michele Clamp
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6.  Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers.

Authors:  Rajeev K Varshney; Wenbin Chen; Yupeng Li; Arvind K Bharti; Rachit K Saxena; Jessica A Schlueter; Mark T A Donoghue; Sarwar Azam; Guangyi Fan; Adam M Whaley; Andrew D Farmer; Jaime Sheridan; Aiko Iwata; Reetu Tuteja; R Varma Penmetsa; Wei Wu; Hari D Upadhyaya; Shiaw-Pyng Yang; Trushar Shah; K B Saxena; Todd Michael; W Richard McCombie; Bicheng Yang; Gengyun Zhang; Huanming Yang; Jun Wang; Charles Spillane; Douglas R Cook; Gregory D May; Xun Xu; Scott A Jackson
Journal:  Nat Biotechnol       Date:  2011-11-06       Impact factor: 54.908

7.  Isoform-specific targeting and interaction domains in human nicotinamide mononucleotide adenylyltransferases.

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8.  Genome-wide patterns of genetic variation among elite maize inbred lines.

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Journal:  Nat Genet       Date:  2010-10-24       Impact factor: 38.330

9.  Characterization of maltase clusters in the genus Drosophila.

Authors:  Marek Gabriško; Stefan Janeček
Journal:  J Mol Evol       Date:  2010-11-17       Impact factor: 2.395

10.  Genome of the Chinese tree shrew.

Authors:  Yu Fan; Zhi-Yong Huang; Chang-Chang Cao; Ce-Shi Chen; Yuan-Xin Chen; Ding-Ding Fan; Jing He; Hao-Long Hou; Li Hu; Xin-Tian Hu; Xuan-Ting Jiang; Ren Lai; Yong-Shan Lang; Bin Liang; Sheng-Guang Liao; Dan Mu; Yuan-Ye Ma; Yu-Yu Niu; Xiao-Qing Sun; Jin-Quan Xia; Jin Xiao; Zhi-Qiang Xiong; Lin Xu; Lan Yang; Yun Zhang; Wei Zhao; Xu-Dong Zhao; Yong-Tang Zheng; Ju-Min Zhou; Ya-Bing Zhu; Guo-Jie Zhang; Jun Wang; Yong-Gang Yao
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919
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