Software for Analyzing Biosequence Data

用于分析生物序列数据的软件

• 批准号: 7111746
• 负责人: Webb Colby Miller
• 金额: $ 90.81万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-08-15 至 2008-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7111746
• 关键词: biochemical evolution; bioengineering /biomedical engineering; computer assisted sequence analysis; computer program /software; computer system design /evaluation; gene mutation; molecular biology information system; nucleic acid sequence

DESCRIPTION (provided by applicant): Projects to sequence vertebrate genomes are proceeding more rapidly than was imagined a few years ago. New computational tools for comparative genome analysis at the nucleotide level are needed to more effectively identify functional but non-protein-coding segments and to dissect mammalian evolution. The Penn State group has excelled at developing such tools. Our PipMaker and MultiPipMaker Web servers set the standard for alignment of user specified genomic sequences, and our Blastz program was chosen to produce high-sensitivity alignments for the Mouse Genome Analysis Consortium. We were also a significant source of biological and statistical expertise within the Consortium, particularly with respect to functional non-coding segments and evolution. We will raise comparative genome studies to a higher level by developing software that accurately identifies the full spectrum of mutational events. Current multiple alignment procedures use one sequence as the reference and hence give an asymmetric and incomplete view of sequence relationships. Our new Generalized Multiple Alignments will provide symmetric and complete views of the alignments, accurately identify kilobase-scale insertions and deletions, and permit any of the species to be used as a reference in subsequent analysis. The results obtained by our new alignment programs will be analyzed using new statistical procedures to more accurately predict the locations of elements that regulate gene transcription, and to measure variation and co-variation of mutational rates along the genome. These computational studies will guide experimental work to confirm regulatory sites and to identify the biological mechanisms that underlie rate variations in neutral evolution. An integral part of this effort will be our continued collaborations with the NISC Comparative Sequencing Program, with the group headed by David Haussler and Jim Kent at the University of California at Santa Cruz, and with the Comparative Chloroplast Genomics Project.

描述（由申请人提供）： 对脊椎动物基因组进行测序的项目比几年前想象的要快。需要在核苷酸水平上进行比较基因组分析的新计算工具，以更有效地识别功能性但非蛋白质编码段并剖析哺乳动物进化。 宾夕法尼亚州立大学在开发此类工具方面表现出色。我们的Pipmaker和MultipipMaker Web服务器设置了用户指定基因组序列对齐的标准，并选择了我们的BLASTZ程序来为小鼠基因组分析联盟产生高敏度比对。我们也是财团内生物学和统计专业知识的重要来源，特别是在功能性非编码段和进化方面。 我们将通过开发准确识别突变事件的整个软件，将比较基因组研究提高到更高的水平。当前的多个比对程序使用一个序列作为参考，因此给出了序列关系的不对称和不完全视图。我们新的广义多个比对将提供对齐对齐的对称和完整视图，准确地识别千目标尺度插入和缺失，并允许任何物种在后续分析中用作参考。我们的新对准程序获得的结果将使用新的统计程序进行分析，以更准确地预测调节基因转录的元素的位置，并测量沿基因组突变率的变异和共同变化。这些计算研究将指导实验性工作以确认调节位点，并确定中性进化速率变化的生物学机制。 这项工作不可或缺的一部分将是我们与NISC比较测序计划的持续合作，由David Haussler和加利福尼亚大学圣克鲁斯分校的Jim Kent领导的小组以及比较叶绿体基因组学项目。