HortGenome Search Engine, a universal genomic search engine for horticultural crops.

Journal

Horticulture research
ISSN: 2662-6810
Titre abrégé: Hortic Res
Pays: England
ID NLM: 101655540

Informations de publication

Date de publication:
Jun 2024
Historique:
received: 01 12 2023
accepted: 27 03 2024
medline: 12 6 2024
pubmed: 12 6 2024
entrez: 12 6 2024
Statut: epublish

Résumé

Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows for the querying of genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 500 horticultural crops. In addition, four commonly used tools, including 'BLAST', 'Batch Query', 'Enrichment analysis', and 'Synteny Viewer' have been developed for efficient mining and analysis of these genomic data.

Identifiants

DOI: 10.1093/hr/uhae100 PMID: 38863996 PMC: PMC11165154
pubmed: 38863996
doi: 10.1093/hr/uhae100
pii: uhae100
pmc: PMC11165154
doi:

Types de publication

Journal Article

Langues

eng

Pagination

uhae100

Informations de copyright

© The Author(s) 2024. Published by Oxford University Press on behalf of Nanjing Agricultural University.

Auteurs

Sen Wang (S)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Shangxiao Wei (S)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Yuling Deng (Y)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Shaoyuan Wu (S)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Haixu Peng (H)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

You Qing (Y)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Xuyang Zhai (X)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Shijie Zhou (S)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Jinrong Li (J)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Hua Li (H)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Yijian Feng (Y)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Yating Yi (Y)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Rui Li (R)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Hui Zhang (H)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.

Yiding Wang (Y)

College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China.

Renlong Zhang (R)

College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China.

Lu Ning (L)

Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.
Library, Beijing University of Agriculture, Beijing 102206, China.

Yuncong Yao (Y)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.

Zhangjun Fei (Z)

Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.
USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.

Yi Zheng (Y)

Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China.
ORCID: 0000-0002-8042-7770

Classifications MeSH