Karen Eilbeck1, Barry Moore, Carson Holt, Mark Yandell. 1. Department of Human genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA. keilbeck@genetics.utah.edu
Abstract
BACKGROUND: The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. RESULTS: In response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases -- H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. CONCLUSION: Our results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management.
BACKGROUND: The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. RESULTS: In response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases -- H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. CONCLUSION: Our results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management.
Authors: G M Rubin; M D Yandell; J R Wortman; G L Gabor Miklos; C R Nelson; I K Hariharan; M E Fortini; P W Li; R Apweiler; W Fleischmann; J M Cherry; S Henikoff; M P Skupski; S Misra; M Ashburner; E Birney; M S Boguski; T Brody; P Brokstein; S E Celniker; S A Chervitz; D Coates; A Cravchik; A Gabrielian; R F Galle; W M Gelbart; R A George; L S Goldstein; F Gong; P Guan; N L Harris; B A Hay; R A Hoskins; J Li; Z Li; R O Hynes; S J Jones; P M Kuehl; B Lemaitre; J T Littleton; D K Morrison; C Mungall; P H O'Farrell; O K Pickeral; C Shue; L B Vosshall; J Zhang; Q Zhao; X H Zheng; S Lewis Journal: Science Date: 2000-03-24 Impact factor: 47.728
Authors: Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; David L Wheeler Journal: Nucleic Acids Res Date: 2007-01 Impact factor: 16.971
Authors: Madeline A Crosby; Joshua L Goodman; Victor B Strelets; Peili Zhang; William M Gelbart Journal: Nucleic Acids Res Date: 2006-11-11 Impact factor: 16.971
Authors: Roderic Guigó; Paul Flicek; Josep F Abril; Alexandre Reymond; Julien Lagarde; France Denoeud; Stylianos Antonarakis; Michael Ashburner; Vladimir B Bajic; Ewan Birney; Robert Castelo; Eduardo Eyras; Catherine Ucla; Thomas R Gingeras; Jennifer Harrow; Tim Hubbard; Suzanna E Lewis; Martin G Reese Journal: Genome Biol Date: 2006-08-07 Impact factor: 13.583
Authors: Tamberlyn Bieri; Darin Blasiar; Philip Ozersky; Igor Antoshechkin; Carol Bastiani; Payan Canaran; Juancarlos Chan; Nansheng Chen; Wen J Chen; Paul Davis; Tristan J Fiedler; Lisa Girard; Michael Han; Todd W Harris; Ranjana Kishore; Raymond Lee; Sheldon McKay; Hans-Michael Müller; Cecilia Nakamura; Andrei Petcherski; Arun Rangarajan; Anthony Rogers; Gary Schindelman; Erich M Schwarz; Will Spooner; Mary Ann Tuli; Kimberly Van Auken; Daniel Wang; Xiaodong Wang; Gary Williams; Richard Durbin; Lincoln D Stein; Paul W Sternberg; John Spieth Journal: Nucleic Acids Res Date: 2006-11-11 Impact factor: 16.971
Authors: MeiYee Law; Kevin L Childs; Michael S Campbell; Joshua C Stein; Andrew J Olson; Carson Holt; Nicholas Panchy; Jikai Lei; Dian Jiao; Carson M Andorf; Carolyn J Lawrence; Doreen Ware; Shin-Han Shiu; Yanni Sun; Ning Jiang; Mark Yandell Journal: Plant Physiol Date: 2014-11-10 Impact factor: 8.340
Authors: Candice N Hirsch; Cory D Hirsch; Alex B Brohammer; Megan J Bowman; Ilya Soifer; Omer Barad; Doron Shem-Tov; Kobi Baruch; Fei Lu; Alvaro G Hernandez; Christopher J Fields; Chris L Wright; Klaus Koehler; Nathan M Springer; Edward Buckler; C Robin Buell; Natalia de Leon; Shawn M Kaeppler; Kevin L Childs; Mark A Mikel Journal: Plant Cell Date: 2016-11-01 Impact factor: 11.277
Authors: David E Jarvis; Yung Shwen Ho; Damien J Lightfoot; Sandra M Schmöckel; Bo Li; Theo J A Borm; Hajime Ohyanagi; Katsuhiko Mineta; Craig T Michell; Noha Saber; Najeh M Kharbatia; Ryan R Rupper; Aaron R Sharp; Nadine Dally; Berin A Boughton; Yong H Woo; Ge Gao; Elio G W M Schijlen; Xiujie Guo; Afaque A Momin; Sónia Negrão; Salim Al-Babili; Christoph Gehring; Ute Roessner; Christian Jung; Kevin Murphy; Stefan T Arold; Takashi Gojobori; C Gerard van der Linden; Eibertus N van Loo; Eric N Jellen; Peter J Maughan; Mark Tester Journal: Nature Date: 2017-02-08 Impact factor: 49.962
Authors: Thomas C Boothby; Jennifer R Tenlen; Frank W Smith; Jeremy R Wang; Kiera A Patanella; Erin Osborne Nishimura; Sophia C Tintori; Qing Li; Corbin D Jones; Mark Yandell; David N Messina; Jarret Glasscock; Bob Goldstein Journal: Proc Natl Acad Sci U S A Date: 2015-11-23 Impact factor: 11.205
Authors: Dario Copetti; Alberto Búrquez; Enriquena Bustamante; Joseph L M Charboneau; Kevin L Childs; Luis E Eguiarte; Seunghee Lee; Tiffany L Liu; Michelle M McMahon; Noah K Whiteman; Rod A Wing; Martin F Wojciechowski; Michael J Sanderson Journal: Proc Natl Acad Sci U S A Date: 2017-10-23 Impact factor: 11.205
Authors: Young-Jun Choi; Santiago Fontenla; Peter U Fischer; Thanh Hoa Le; Alicia Costábile; David Blair; Paul J Brindley; Jose F Tort; Miguel M Cabada; Makedonka Mitreva Journal: Mol Biol Evol Date: 2020-01-01 Impact factor: 16.240
Authors: Michael S Campbell; MeiYee Law; Carson Holt; Joshua C Stein; Gaurav D Moghe; David E Hufnagel; Jikai Lei; Rujira Achawanantakun; Dian Jiao; Carolyn J Lawrence; Doreen Ware; Shin-Han Shiu; Kevin L Childs; Yanni Sun; Ning Jiang; Mark Yandell Journal: Plant Physiol Date: 2013-12-04 Impact factor: 8.340