Plant Growth Regulation

, Volume 70, Issue 2, pp 199–206

Apple gene function and gene family database: an integrated bioinformatics database for apple research

  • Shizhong Zhang
  • Guang Hui Chen
  • Yukun Liu
  • Hao Chen
  • Guodong Yang
  • Xiaowei Yuan
  • Zesheng Jiang
  • Huairui Shu
Brief Communication

Abstract

The apple (Malus domestica) is one of the most economically important fruit crops in the world, due its importance to human nutrition and health. To analyze the function and evolution of different apple genes, we developed apple gene function and gene family database (AppleGFDB) for collecting, storing, arranging, and integrating functional genomics information of the apple. The AppleGFDB provides several layers of information about the apple genes, including nucleotide and protein sequences, chromosomal locations, gene structures, and any publications related to these annotations. To further analyze the functional genomics data of apple genes, the AppleGFDB was designed to enable users to easily retrieve information through a suite of interfaces, including gene ontology, protein domain and InterPro. In addition, the database provides tools for analyzing the expression profiles and microRNAs of the apple. Moreover, all of the analyzed and collected data can be downloaded from the database. The database can also be accessed using a convenient web server that supports a full-text search, a BLAST sequence search, and database browsing. Furthermore, to facilitate cooperation among apple researchers, AppleGFDB is presented in a user-interactive platform, which provides users with the opportunity to modify apple gene annotations and submit publication information for related genes. AppleGFDB is available at http://www.applegene.org or http://gfdb.sdau.edu.cn/.

Keywords

Malus domestica genome AppleGFDB Database 

Abbreviations

ABA

Abscisic acid

ACC

1-aminocyclopropane-1-carboxylic acid

AppleGFDB

Apple gene function and gene family database

BLAST

Basic local alignment search tool

CDD

Conserved domain database

EBI

European Bioinformatics Institute

ESTs

Expressed sequence tags

GDR

Genome database for rosaceae

GEO

Gene expression omnibus

GO

Gene ontology

HMM

Hidden Markov model

IASMA

Istituto agrario di san michele all’adige

NCBI

National center for biotechnology information

PDB

Protein data bank

PlnTFDB

Plant transcription factor database

SMART

Simple modular architecture research tool

TAIR

The arabidopsis information resource

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Shizhong Zhang
    • 1
  • Guang Hui Chen
    • 2
  • Yukun Liu
    • 3
  • Hao Chen
    • 2
  • Guodong Yang
    • 2
  • Xiaowei Yuan
    • 2
  • Zesheng Jiang
    • 1
  • Huairui Shu
    • 1
  1. 1.National Research Center for Apple Engineering and Technology, College of Horticulture Science and TechnologyShandong Agricultural UniversityTai’anChina
  2. 2.State Key Laboratory of Crop Biology, College of Life ScienceShandong Agricultural UniversityTai’anChina
  3. 3.Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of EducationSouthwest Forestry UniversityKunmingChina

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