Development and maintenance of bioinformatics tools for mouse biology

小鼠生物学生物信息学工具的开发和维护

• 批准号: 7732289
• 负责人: Minoru Ko
• 金额: $ 31.17万
• 依托单位: NATIONAL INSTITUTE ON AGING
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7732289
• 关键词: Algorithms; Alternative Splicing; Base Sequence; Binding; Binding Sites; Bioinformatics; Biological Models; Biology; Color; Communities; Computer software; Consensus; DNA Microarray Chip; DNA Microarray format; Data; Data Analyses; Databases; Development; Genes; Genome; Goals; Human Biology; Internet; Maintenance; Maps; Mining; Molecular Profiling; Mus; Online Systems; Quality Control; Range; Regenerative Medicine; Research; Resources; Software Tools; Transcript; Update; Work; base; chromatin immunoprecipitation; genome sequencing; indexing; mouse genome; reproductive; tool; transcription factor; user-friendly

In our previous work, we developed four major bioinformatics tools/databases: (1) a web-based ANOVA-FDR software to provide user-friendly microarray data analysis (http://lgsun.grc.nia.nih.gov/ANOVA/); (2) an algorithm and a fully-automated computational pipeline for transcript assembly from expressed sequences aligned to the mouse genome; (3) a web-based browser to visualize all transcripts and alternative spliced forms of mouse genes (NIA Mouse Gene Index: http://lgsun.grc.nia.nih.gov/geneindex/mm9/); and (4) an web-based database and tool to visualize and map transcription factor binding sites of the mouse genome (CisView: http://lgsun.grc.nia.nih.gov/geneindex/mm6/cisview.html). The unrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine. During the last year, we have updated all of these databases based on the latest mouse genome sequence assembly. We are currently developing tools to carry out quality control (QC) of 2-color DNA microarray results and a software tool to identify consensus transcription factor binding sequences based on genome-wide chromatin immunoprecipitation analysis (ChIP-Seq) and expression profiling data.

在我们之前的工作中，我们开发了四种主要的生物信息学工具/数据库：（1）基于网络的ANOVA-FDR软件，提供用户友好的微阵列数据分析（http://lgsun.grc.nia.nih.gov/ANOVA/ ）； (2) 用于从与小鼠基因组比对的表达序列组装转录物的算法和全自动计算管道； (3) 基于网络的浏览器，用于可视化小鼠基因的所有转录本和选择性剪接形式（NIA小鼠基因索引：http://lgsun.grc.nia.nih.gov/geneindex/mm9/）； (4) 基于网络的数据库和工具，用于可视化和绘制小鼠基因组转录因子结合位点的图谱（CisView：http://lgsun.grc.nia.nih.gov/geneindex/mm6/cisview.html）。社区不受限制地获取资源可以加速广泛的研究，特别是在生殖和再生医学方面。 去年，我们根据最新的小鼠基因组序列组装更新了所有这些数据库。我们目前正在开发对 2 色 DNA 微阵列结果进行质量控制 (QC) 的工具，以及基于全基因组染色质免疫沉淀分析 (ChIP-Seq) 和表达谱数据识别共有转录因子结合序列的软件工具。