CannSeek？是的，我们能行！一个用于……的开源单核苷酸多态性数据库及分析平台。（原文中“for”后面内容不完整）

CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for .

作者信息

Mansueto Locedie, McNally Kenneth L, Kretzschmar Tobias, Mauleon Ramil

机构信息

Southern Cross University, Military Road, Lismore New South Wales 2480, Australia.

International Rice Research Institute, Pili Drive, Los Baños Laguna 4031, Philippines.

出版信息

GigaByte. 2024 Oct 8;2024:gigabyte135. doi: 10.46471/gigabyte.135. eCollection 2024.

DOI:10.46471/gigabyte.135

PMID:39416656

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11480739/

Abstract

UNLABELLED

A growing interest in uses for food, fiber, and medicine, and recent changes in regulations have spurred numerous genomic studies of this once-prohibited plant. Cannabis research uses Next Generation Sequencing technologies for genomics and transcriptomics. While other crops have genome portals enabling access and analysis of numerous genotyping data from diverse accessions, leading to the discovery of alleles for important traits, this is absent for cannabis. The CannSeek web portal aims to address this gap. Single nucleotide polymorphism datasets were generated by identifying genome variants from public resequencing data and genome assemblies. Results and accompanying trait data are hosted in the CannSeek web application, built using the Rice SNP-Seek infrastructure with improvements to allow multiple reference genomes and provide a web-service Application Programming Interface. The tools built into the portal allow phylogenetic analyses, varietal grouping and identifications, and favorable haplotype discovery for cannabis accessions using public sequencing data.

AVAILABILITY AND IMPLEMENTATION

The CannSeek portal is available at https://icgrc.info/cannseek, https://icgrc.info/genotype_viewer.

摘要

未标注

对大麻在食品、纤维和医药方面用途的兴趣日益增长，以及近期法规的变化，促使人们对这种曾经被禁止的植物进行了大量基因组研究。大麻研究使用下一代测序技术进行基因组学和转录组学研究。虽然其他作物有基因组门户，可用于访问和分析来自不同种质的大量基因分型数据，从而发现重要性状的等位基因，但大麻却没有这样的门户。CannSeek网络门户旨在填补这一空白。通过从公共重测序数据和基因组组装中识别基因组变异，生成了单核苷酸多态性数据集。结果及相关性状数据存储在CannSeek网络应用程序中，该程序基于水稻SNP-Seek基础设施构建，并进行了改进，以允许使用多个参考基因组并提供网络服务应用程序编程接口。该门户内置的工具可利用公共测序数据对大麻种质进行系统发育分析、品种分组和鉴定，以及发现有利单倍型。