Making whole genome multiple alignments usable for biologists

被引：28
作者：
Blankenberg, Daniel [3 ,4 ]
Taylor, James [1 ,2 ]
Nekrutenko, Anton [3 ,4 ]
机构：
[1] Emory Univ, Dept Biol, Atlanta, GA 30322 USA
[2] Emory Univ, Dept Math & Comp Sci, Atlanta, GA 30322 USA
[3] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
[4] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA
来源：
BIOINFORMATICS | 2011年 / 27卷 / 17期
基金：
美国国家卫生研究院; 美国国家科学基金会;
关键词：
BROWSER; UCSC;
D O I：
10.1093/bioinformatics/btr398
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Here we describe a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface.
引用
收藏
页码：2426 / 2428
页数：3
相关论文
共 9 条
  • [1] Galaxy CloudMan: delivering cloud compute clusters
    Afgan, Enis
    Baker, Dannon
    Coraor, Nate
    Chapman, Brad
    Nekrutenko, Anton
    Taylor, James
    [J]. BMC BIOINFORMATICS, 2010, 11
  • [2] A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
    Blankenberg, Daniel
    Taylor, James
    Schenck, Ian
    He, Jianbin
    Zhang, Yi
    Ghent, Matthew
    Veeraraghavan, Narayanan
    Albert, Istvan
    Miller, Webb
    Makova, Kateryna D.
    Hardison, Ross C.
    Nekrutenko, Anton
    [J]. GENOME RESEARCH, 2007, 17 (06) : 960 - 964
  • [3] Blankenberg Daniel, 2010, Curr Protoc Mol Biol, VChapter 19, DOI 10.1002/0471142727.mb1910s89
  • [4] The UCSC Genome Browser database: update 2011
    Fujita, Pauline A.
    Rhead, Brooke
    Zweig, Ann S.
    Hinrichs, Angie S.
    Karolchik, Donna
    Cline, Melissa S.
    Goldman, Mary
    Barber, Galt P.
    Clawson, Hiram
    Coelho, Antonio
    Diekhans, Mark
    Dreszer, Timothy R.
    Giardine, Belinda M.
    Harte, Rachel A.
    Hillman-Jackson, Jennifer
    Hsu, Fan
    Kirkup, Vanessa
    Kuhn, Robert M.
    Learned, Katrina
    Li, Chin H.
    Meyer, Laurence R.
    Pohl, Andy
    Raney, Brian J.
    Rosenbloom, Kate R.
    Smith, Kayla E.
    Haussler, David
    Kent, W. James
    [J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D876 - D882
  • [5] Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    Goecks, Jeremy
    Nekrutenko, Anton
    Taylor, James
    [J]. GENOME BIOLOGY, 2010, 11 (08):
  • [6] The UCSC Table Browser data retrieval tool
    Karolchik, D
    Hinrichs, AS
    Furey, TS
    Roskin, KM
    Sugnet, CW
    Haussler, D
    Kent, WJ
    [J]. NUCLEIC ACIDS RESEARCH, 2004, 32 : D493 - D496
  • [7] The human genome browser at UCSC
    Kent, WJ
    Sugnet, CW
    Furey, TS
    Roskin, KM
    Pringle, TH
    Zahler, AM
    Haussler, D
    [J]. GENOME RESEARCH, 2002, 12 (06) : 996 - 1006
  • [8] 28-way vertebrate alignment and conservation track in the UCSC Genome Browser
    Miller, Webb
    Rosenbloom, Kate
    Hardison, Ross C.
    Hou, Minmei
    Taylor, James
    Raney, Brian
    Burhans, Richard
    King, David C.
    Baertsch, Robert
    Blankenberg, Daniel
    Pond, Sergei L. Kosakovsky
    Nekrutenko, Anton
    Giardine, Belinda
    Harris, Robert S.
    Diekhans, Svitlana Tyekucheva Mark
    Diekhans, Mark
    Pringle, Thomas H.
    Murphy, William J.
    Lesk, Arthur
    Weinstock, George M.
    Lindblad-Toh, Kerstin
    Gibbs, Richard A.
    Lander, Eric S.
    Siepel, Adam
    Haussler, David
    Kent, W. James
    [J]. GENOME RESEARCH, 2007, 17 (12) : 1797 - 1808
  • [9] Taylor J., 2007, Curr Protoc Bioinformatics, V19
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