新疆天山雪莲转录组注解知识库
# 共同第一作者
收稿日期: 2016-05-25
录用日期: 2016-09-18
网络出版日期: 2017-05-05
基金资助
基金项目: 国家自然科学基金(No.C020406)
The Sasussured involucrata Transcriptome Knowledge Base
# Co-first authors
Received date: 2016-05-25
Accepted date: 2016-09-18
Online published: 2017-05-05
新疆天山雪莲(Sasussured involucrata)具有较高的极端低温耐受特性, 为低温耐受机制研究提供了一种非常好的模式植物。新疆天山雪莲转录组注解知识库(http://www.shengtingbiology.com/SaussureaKBase/index.jsp)是基于网络数据资源的综合性数据库, 由html、Perl、Perl CGI/DBD/DBI、Java和JavaScript编程所设计的前端界面和用于数据存取、注释及管理的后端数据库管理系统PostgrelSQL构成。知识库包含基因组数据、转录组原始数据、质量控制数据、GC含量、功能基因序列及注释、功能基因代谢通路、功能基因的注释统计、雪莲与其它物种的转录组或基因组比较分析数据和生物分析软件包等资源。该数据库不仅有利于低温功能基因组学及低温耐受机制研究, 而且为冷耐受性状物种的分子育种提供基因资源平台和理论依据。
李锦, 严潘瑶, 钱飞箭, 邱宝义, 夏雯雯, 牟晓威, 邱丽娟, 林忠平, 陈铭, 祝建波, 陈贤丰 . 新疆天山雪莲转录组注解知识库[J]. 植物学报, 2017 , 52(4) : 530 -538 . DOI: 10.11983/CBB16113
The Sasussured involucrata possesses high cold-tolerance capacity, which could be a good experimental model for investigating the cold tolerance mechanism. The S. involucrata Transcriptome Knowledge Base (SITKB) (http://www.shengtingsystemsbiology.com/SaussureaKBase/) is a web-based comprehensive database system implemented via html, Perl and Perl CGI/DBI/DBD, Java and JavaScript programming languages on the web front end and PostgrelSQL Relational Database Management System as the backend for data, annotation and knowledge management. SITKB systems was designated to facilitate cold-tolerance gene mining and knowledge discovery and hosts useful knowledge sets such as datasets of raw sequence data quality control, GC contents of raw and assembled DNA sequences, functional annotation of the assembled contigs, assignment of metabolic pathways to the contigs with coding potential, statistics on the rate of meaningful annotation, and blast comparison against other plant transcriptomes or genomes. The knowledge base system also contains a set of software packages for bioinformatics analysis against its stored datasets. This new knowledge base would provide a resource for data mining and knowledge discovery of the functional genes and pathways responsive to cold perturbation and also enhance the capability for elucidating the cold tolerance mechanism. It also offers genomic data resources and a theoretical foundation to facilitate the molecular breeding of cold tolerant crops.
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