FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

被引：299

作者：

dos Santos, Gilberto ^{[1
]}

Schroeder, Andrew J. ^{[1
]}

Goodman, Joshua L. ^{[2
]}

Strelets, Victor B. ^{[2
]}

Crosby, Madeline A. ^{[1
]}

Thurmond, Jim ^{[2
]}

Emmert, David B. ^{[1
]}

Gelbart, William M. ^{[1
]}

机构：

[1] Harvard Univ, Biol Labs, Cambridge, MA 02138 USA

[2] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / D1期

基金：

英国医学研究理事会; 美国国家卫生研究院;

关键词：

SEQUENCE; GENERATION; BROWSER;

D O I：

10.1093/nar/gku1099

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly. In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can be viewed in FlyBase (http://flybase.org) and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.

引用

页码：D690 / D697

页数：8

共 24 条

[11] The developmental transcriptome of Drosophila melanogaster [J].

Graveley, Brenton R. ;

Brooks, Angela N. ;

Carlson, JosephW. ;

Duff, Michael O. ;

Landolin, Jane M. ;

Yang, Li ;

Artieri, Carlo G. ;

van Baren, Marijke J. ;

Boley, Nathan ;

Booth, Benjamin W. ;

Brown, James B. ;

Cherbas, Lucy ;

Davis, Carrie A. ;

Dobin, Alex ;

Li, Renhua ;

Lin, Wei ;

Malone, John H. ;

Mattiuzzo, Nicolas R. ;

Miller, David ;

Sturgill, David ;

Tuch, Brian B. ;

Zaleski, Chris ;

Zhang, Dayu ;

Blanchette, Marco ;

Dudoit, Sandrine ;

Eads, Brian ;

Green, Richard E. ;

Hammonds, Ann ;

Jiang, Lichun ;

Kapranov, Phil ;

Langton, Laura ;

Perrimon, Norbert ;

Sandler, Jeremy E. ;

Wan, Kenneth H. ;

Willingham, Aarron ;

Zhang, Yu ;

Zou, Yi ;

Andrews, Justen ;

Bickel, Peter J. ;

Brenner, Steven E. ;

Brent, Michael R. ;

Cherbas, Peter ;

Gingeras, Thomas R. ;

Hoskins, Roger A. ;

Kaufman, Thomas C. ;

Oliver, Brian ;

Celniker, Susan E. .

NATURE, 2011, 471 (7339) :473-479

[12] Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster [J].

He, Bing ;

Caudy, Amy ;

Parsons, Lance ;

Rosebrock, Adam ;

Pane, Attilio ;

Raj, Sandeep ;

Wieschaus, Eric .

GENOME RESEARCH, 2012, 22 (12) :2507-2519

[13] Sequence finishing and mapping of Drosophila melanogaster heterochromatin [J].

Hoskins, Roger A. ;

Carlson, Joseph W. ;

Kennedy, Cameron ;

Acevedo, David ;

Evans-Holm, Martha ;

Frise, Erwin ;

Wan, Kenneth H. ;

Park, Soo ;

Mendez-Lago, Maria ;

Rossi, Fabrizio ;

Villasante, Alfredo ;

Dimitri, Patrizio ;

Karpen, Gary H. ;

Celniker, Susan E. .

SCIENCE, 2007, 316 (5831) :1625-1628

[14] Splign: algorithms for computing spliced alignments with identification of paralogs [J].

Kapustin, Yuri ;

Souvorov, Alexander ;

Tatusova, Tatiana ;

Lipman, David .

BIOLOGY DIRECT, 2008, 3 (1)

[15] The UCSC Genome Browser database: 2014 update [J].

Karolchik, Donna ;

Barber, Galt P. ;

Casper, Jonathan ;

Clawson, Hiram ;

Cline, Melissa S. ;

Diekhans, Mark ;

Dreszer, Timothy R. ;

Fujita, Pauline A. ;

Guruvadoo, Luvina ;

Haeussler, Maximilian ;

Harte, Rachel A. ;

Heitner, Steve ;

Hinrichs, Angie S. ;

Learned, Katrina ;

Lee, Brian T. ;

Li, Chin H. ;

Raney, Brian J. ;

Rhead, Brooke ;

Rosenbloom, Kate R. ;

Sloan, Cricket A. ;

Speir, Matthew L. ;

Zweig, Ann S. ;

Haussler, David ;

Kuhn, Robert M. ;

Kent, W. James .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D764-D770

[16] Mapping and quantifying mammalian transcriptomes by RNA-Seq [J].

Mortazavi, Ali ;

Williams, Brian A. ;

McCue, Kenneth ;

Schaeffer, Lorian ;

Wold, Barbara .

NATURE METHODS, 2008, 5 (07) :621-628

[17] A Chado case study: an ontology-based modular schema for representing genome-associated biological information [J].

Mungall, Christopher J. ;

Emmert, David B. .

BIOINFORMATICS, 2007, 23 (13) :I337-I346

[18] A whole-genome assembly of Drosophila [J].

Myers, EW ;

Sutton, GG ;

Delcher, AL ;

Dew, IM ;

Fasulo, DP ;

Flanigan, MJ ;

Kravitz, SA ;

Mobarry, CM ;

Reinert, KHJ ;

Remington, KA ;

Anson, EL ;

Bolanos, RA ;

Chou, HH ;

Jordan, CM ;

Halpern, AL ;

Lonardi, S ;

Beasley, EM ;

Brandon, RC ;

Chen, L ;

Dunn, PJ ;

Lai, ZW ;

Liang, Y ;

Nusskern, DR ;

Zhan, M ;

Zhang, Q ;

Zheng, XQ ;

Rubin, GM ;

Adams, MD ;

Venter, JC .

SCIENCE, 2000, 287 (5461) :2196-2204

[19] IMPROVED TOOLS FOR BIOLOGICAL SEQUENCE COMPARISON [J].

PEARSON, WR ;

LIPMAN, DJ .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1988, 85 (08) :2444-2448

[20] RefSeq: an update on mammalian reference sequences [J].

Pruitt, Kim D. ;

Brown, Garth R. ;

Hiatt, Susan M. ;

Thibaud-Nissen, Francoise ;

Astashyn, Alexander ;

Ermolaeva, Olga ;

Farrell, Catherine M. ;

Hart, Jennifer ;

Landrum, Melissa J. ;

McGarvey, Kelly M. ;

Murphy, Michael R. ;

O'Leary, Nuala A. ;

Pujar, Shashikant ;

Rajput, Bhanu ;

Rangwala, Sanjida H. ;

Riddick, Lillian D. ;

Shkeda, Andrei ;

Sun, Hanzhen ;

Tamez, Pamela ;

Tully, Raymond E. ;

Wallin, Craig ;

Webb, David ;

Weber, Janet ;

Wu, Wendy ;

DiCuccio, Michael ;

Kitts, Paul ;

Maglott, Donna R. ;

Murphy, Terence D. ;

Ostell, James M. .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D756-D763

← 1 2 3 →