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Literature DB >> 19439563

Apollo: a community resource for genome annotation editing.

Ed Lee¹, Nomi Harris, Mark Gibson, Raymond Chetty, Suzanna Lewis.

Abstract

SUMMARY: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. AVAILABILITY: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.

Mesh：

Year: 2009 PMID： 19439563 PMCID： PMC2705230 DOI： 10.1093/bioinformatics/btp314

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

10 in total

1. The UCSC Genome Browser Database.

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Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

2. The generic genome browser: a building block for a model organism system database.

Authors: Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal: Genome Res Date: 2002-10 Impact factor: 9.043

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Journal: J Mol Biol Date: 1990-10-05 Impact factor: 5.469

4. The FlyBase database of the Drosophila genome projects and community literature.

Authors:
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

5. A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

Authors: Christopher J Mungall; David B Emmert
Journal: Bioinformatics Date: 2007-07-01 Impact factor: 6.937

6. The Sequence Ontology: a tool for the unification of genome annotations.

Authors: Karen Eilbeck; Suzanna E Lewis; Christopher J Mungall; Mark Yandell; Lincoln Stein; Richard Durbin; Michael Ashburner
Journal: Genome Biol Date: 2005-04-29 Impact factor: 13.583

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9. nGASP--the nematode genome annotation assessment project.

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Review 10. Apollo: a sequence annotation editor.

Authors: S E Lewis; S M J Searle; N Harris; M Gibson; V Lyer; J Richter; C Wiel; L Bayraktaroglu; E Birney; M A Crosby; J S Kaminker; B B Matthews; S E Prochnik; C D Smithy; J L Tupy; G M Rubin; S Misra; C J Mungall; M E Clamp
Journal: Genome Biol Date: 2002-12-23 Impact factor: 13.583

10 in total

33 in total

1. Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication.

Authors: Sean K McKenzie; Ingrid Fetter-Pruneda; Vanessa Ruta; Daniel J C Kronauer
Journal: Proc Natl Acad Sci U S A Date: 2016-11-22 Impact factor: 11.205

2. Mycobacteriophage Marvin: a new singleton phage with an unusual genome organization.

Authors: Catherine Mageeney; Welkin H Pope; Melinda Harrison; Deborah Moran; Trevor Cross; Deborah Jacobs-Sera; Roger W Hendrix; David Dunbar; Graham F Hatfull
Journal: J Virol Date: 2012-02-22 Impact factor: 5.103

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Authors: Ramana Madupu; Lauren M Brinkac; Jennifer Harrow; Laurens G Wilming; Ulrike Böhme; Philippe Lamesch; Linda I Hannick
Journal: Database (Oxford) Date: 2010-02-18 Impact factor: 3.451

4. Genomic information infrastructure after the deluge.

Authors: Julian Parkhill; Ewan Birney; Paul Kersey
Journal: Genome Biol Date: 2010-07-26 Impact factor: 13.583

5. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Authors: Welkin H Pope; Deborah Jacobs-Sera; Daniel A Russell; Craig L Peebles; Zein Al-Atrache; Turi A Alcoser; Lisa M Alexander; Matthew B Alfano; Samantha T Alford; Nichols E Amy; Marie D Anderson; Alexander G Anderson; Andrew A S Ang; Manuel Ares; Amanda J Barber; Lucia P Barker; Jonathan M Barrett; William D Barshop; Cynthia M Bauerle; Ian M Bayles; Katherine L Belfield; Aaron A Best; Agustin Borjon; Charles A Bowman; Christine A Boyer; Kevin W Bradley; Victoria A Bradley; Lauren N Broadway; Keshav Budwal; Kayla N Busby; Ian W Campbell; Anne M Campbell; Alyssa Carey; Steven M Caruso; Rebekah D Chew; Chelsea L Cockburn; Lianne B Cohen; Jeffrey M Corajod; Steven G Cresawn; Kimberly R Davis; Lisa Deng; Dee R Denver; Breyon R Dixon; Sahrish Ekram; Sarah C R Elgin; Angela E Engelsen; Belle E V English; Marcella L Erb; Crystal Estrada; Laura Z Filliger; Ann M Findley; Lauren Forbes; Mark H Forsyth; Tyler M Fox; Melissa J Fritz; Roberto Garcia; Zindzi D George; Anne E Georges; Christopher R Gissendanner; Shannon Goff; Rebecca Goldstein; Kobie C Gordon; Russell D Green; Stephanie L Guerra; Krysta R Guiney-Olsen; Bridget G Guiza; Leila Haghighat; Garrett V Hagopian; Catherine J Harmon; Jeremy S Harmson; Grant A Hartzog; Samuel E Harvey; Siping He; Kevin J He; Kaitlin E Healy; Ellen R Higinbotham; Erin N Hildebrandt; Jason H Ho; Gina M Hogan; Victoria G Hohenstein; Nathan A Holz; Vincent J Huang; Ericka L Hufford; Peter M Hynes; Arrykka S Jackson; Erica C Jansen; Jonathan Jarvik; Paul G Jasinto; Tuajuanda C Jordan; Tomas Kasza; Murray A Katelyn; Jessica S Kelsey; Larisa A Kerrigan; Daryl Khaw; Junghee Kim; Justin Z Knutter; Ching-Chung Ko; Gail V Larkin; Jennifer R Laroche; Asma Latif; Kohana D Leuba; Sequoia I Leuba; Lynn O Lewis; Kathryn E Loesser-Casey; Courtney A Long; A Javier Lopez; Nicholas Lowery; Tina Q Lu; Victor Mac; Isaac R Masters; Jazmyn J McCloud; Molly J McDonough; Andrew J Medenbach; Anjali Menon; Rachel Miller; Brandon K Morgan; Patrick C Ng; Elvis Nguyen; Katrina T Nguyen; Emilie T Nguyen; Kaylee M Nicholson; Lindsay A Parnell; Caitlin E Peirce; Allison M Perz; Luke J Peterson; Rachel E Pferdehirt; Seegren V Philip; Kit Pogliano; Joe Pogliano; Tamsen Polley; Erica J Puopolo; Hannah S Rabinowitz; Michael J Resiss; Corwin N Rhyan; Yetta M Robinson; Lauren L Rodriguez; Andrew C Rose; Jeffrey D Rubin; Jessica A Ruby; Margaret S Saha; James W Sandoz; Judith Savitskaya; Dale J Schipper; Christine E Schnitzler; Amanda R Schott; J Bradley Segal; Christopher D Shaffer; Kathryn E Sheldon; Erica M Shepard; Jonathan W Shepardson; Madav K Shroff; Jessica M Simmons; Erika F Simms; Brandy M Simpson; Kathryn M Sinclair; Robert L Sjoholm; Ingrid J Slette; Blaire C Spaulding; Clark L Straub; Joseph Stukey; Trevor Sughrue; Tin-Yun Tang; Lyons M Tatyana; Stephen B Taylor; Barbara J Taylor; Louise M Temple; Jasper V Thompson; Michael P Tokarz; Stephanie E Trapani; Alexander P Troum; Jonathan Tsay; Anthony T Tubbs; Jillian M Walton; Danielle H Wang; Hannah Wang; John R Warner; Emilie G Weisser; Samantha C Wendler; Kathleen A Weston-Hafer; Hilary M Whelan; Kurt E Williamson; Angelica N Willis; Hannah S Wirtshafter; Theresa W Wong; Phillip Wu; Yun jeong Yang; Brandon C Yee; David A Zaidins; Bo Zhang; Melina Y Zúniga; Roger W Hendrix; Graham F Hatfull
Journal: PLoS One Date: 2011-01-27 Impact factor: 3.240

6. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.

Authors: C A D'Souza; J W Kronstad; G Taylor; R Warren; M Yuen; G Hu; W H Jung; A Sham; S E Kidd; K Tangen; N Lee; T Zeilmaker; J Sawkins; G McVicker; S Shah; S Gnerre; A Griggs; Q Zeng; K Bartlett; W Li; X Wang; J Heitman; J E Stajich; J A Fraser; W Meyer; D Carter; J Schein; M Krzywinski; K J Kwon-Chung; A Varma; J Wang; R Brunham; M Fyfe; B F F Ouellette; A Siddiqui; M Marra; S Jones; R Holt; B W Birren; J E Galagan; C A Cuomo
Journal: MBio Date: 2011-02-08 Impact factor: 7.867

7. FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum.

Authors: Philip Wong; Mathias Walter; Wanseon Lee; Gertrud Mannhaupt; Martin Münsterkötter; Hans-Werner Mewes; Gerhard Adam; Ulrich Güldener
Journal: Nucleic Acids Res Date: 2010-11-04 Impact factor: 16.971

8. Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4.

Authors: Welkin H Pope; Christina M Ferreira; Deborah Jacobs-Sera; Robert C Benjamin; Ariangela J Davis; Randall J DeJong; Sarah C R Elgin; Forrest R Guilfoile; Mark H Forsyth; Alexander D Harris; Samuel E Harvey; Lee E Hughes; Peter M Hynes; Arrykka S Jackson; Marilyn D Jalal; Elizabeth A MacMurray; Coreen M Manley; Molly J McDonough; Jordan L Mosier; Larissa J Osterbann; Hannah S Rabinowitz; Corwin N Rhyan; Daniel A Russell; Margaret S Saha; Christopher D Shaffer; Stephanie E Simon; Erika F Sims; Isabel G Tovar; Emilie G Weisser; John T Wertz; Kathleen A Weston-Hafer; Kurt E Williamson; Bo Zhang; Steven G Cresawn; Paras Jain; Mariana Piuri; William R Jacobs; Roger W Hendrix; Graham F Hatfull
Journal: PLoS One Date: 2011-10-28 Impact factor: 3.240

9. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.

Authors: Chang Liu; Linchun Shi; Yingjie Zhu; Haimei Chen; Jianhui Zhang; Xiaohan Lin; Xiaojun Guan
Journal: BMC Genomics Date: 2012-12-20 Impact factor: 3.969

10. From manual curation to visualization of gene families and networks across Solanaceae plant species.

Authors: Anuradha Pujar; Naama Menda; Aureliano Bombarely; Jeremy D Edwards; Susan R Strickler; Lukas A Mueller
Journal: Database (Oxford) Date: 2013-05-15 Impact factor: 3.451