Databases and bioinformatics tools for rice research

被引：9
作者：
Garg, Priyanka [1 ]
Jaiswal, Pankaj [1 ]
机构：
[1] Oregon State Univ, Dept Bot & Plant Pathol, 2082 Cordley Hall, Corvallis, OR 97331 USA
来源：
CURRENT PLANT BIOLOGY | 2016年 / 7-8卷
基金：
美国国家科学基金会;
关键词：
Biological database; Rice; Gene expression; Biocuration; Ontology; Pathways;
D O I：
10.1016/j.cpb.2016.12.006
中图分类号：
Q94 [植物学];
学科分类号：
071001 ;
摘要：
Rice is one of the most important agricultural crop in the world and widely studied model plant. The completion of whole genome sequence of rice (Oryza sativa) and high-throughput experimental platforms have led to the generation of the tremendous amount of data, and development of the specialized databases and bioinformatics tools for data processing, efficient organization, analysis, and visualization. In this article, we discuss a collection of biological databases that host genomics data on sequence, gene expression, genetic variation, gene-interactomes, and pathways, and facilitate data analysis and visualization. (C) 2016 The Authors. Published by Elsevier B.V.
引用
收藏
页码：39 / 52
页数：14
相关论文
共 111 条
  • [1] Afgan E., NUCL ACIDS RES, V44
  • [2] The Ensembl gene annotation system
    Aken, Bronwen L.
    Ayling, Sarah
    Barrell, Daniel
    Clarke, Laura
    Curwen, Valery
    Fairley, Susan
    Banet, Julio Fernandez
    Billis, Konstantinos
    Giron, Carlos Garcia
    Hourlier, Thibaut
    Howe, Kevin
    Kahari, Andreas
    Kokocinski, Felix
    Martin, Fergal J.
    Murphy, Daniel N.
    Nag, Rishi
    Ruffier, Magali
    Schuster, Michael
    Tang, Y. Amy
    Vogel, Jan-Hinnerk
    White, Simon
    Zadissa, Amonida
    Flicek, Paul
    Searle, Stephen M. J.
    [J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2016,
  • [3] SNP-Seek database of SNPs derived from 3000 rice genomes
    Alexandrov, Nickolai
    Tai, Shuaishuai
    Wang, Wensheng
    Mansueto, Locedie
    Palis, Kevin
    Fuentes, Roven Rommel
    Ulat, Victor Jun
    Chebotarov, Dmytro
    Zhang, Gengyun
    Li, Zhikang
    Mauleon, Ramil
    Hamilton, Ruaraidh Sackville
    McNally, Kenneth L.
    [J]. NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) : D1023 - D1027
  • [4] DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species
    Alter, Svenja
    Bader, Kai C.
    Spannagl, Manuel
    Wang, Yu
    Bauer, Eva
    Schoen, Chris-Carolin
    Mayer, Klaus F. X.
    [J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2015,
  • [5] FAIR principles for data stewardship
    不详
    [J]. NATURE GENETICS, 2016, 48 (04) : 343 - 343
  • [6] ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression
    Aoki, Yuichi
    Okamura, Yasunobu
    Tadaka, Shu
    Kinoshita, Kengo
    Obayashi, Takeshi
    [J]. PLANT AND CELL PHYSIOLOGY, 2016, 57 (01) : e5
  • [7] New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana
    Austin, Ryan S.
    Hiu, Shu
    Waese, Jamie
    Ierullo, Matthew
    Pasha, Asher
    Wang, Ting Ting
    Fan, Jim
    Foong, Curtis
    Breit, Robert
    Desveaux, Darrell
    Moses, Alan
    Provart, Nicholas J.
    [J]. PLANT JOURNAL, 2016, 88 (03) : 490 - 504
  • [8] Benson DA, 2011, NUCLEIC ACIDS RES, V39, pD32, DOI [10.1093/nar/gkt1030, 10.1093/nar/gkq1079, 10.1093/nar/gkw1070, 10.1093/nar/gkx1094, 10.1093/nar/gks1195, 10.1093/nar/gkr1202, 10.1093/nar/gkp1024, 10.1093/nar/gkn723]
  • [9] The Protein Data Bank
    Berman, HM
    Westbrook, J
    Feng, Z
    Gilliland, G
    Bhat, TN
    Weissig, H
    Shindyalov, IN
    Bourne, PE
    [J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 235 - 242
  • [10] Bolser D, 2016, METHODS MOL BIOL, V1374, P115, DOI 10.1007/978-1-4939-3167-5_6
12345678910