CAREER: Computational Protein Function Annotation for Metagenomics

“该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。“这是一个职业奖给印第安纳州大学信息学系的Yuzhen Ye博士。叶博士是第二年的终身助理教授。宏基因组序列数量巨大，并且如在实验室中获得的，片段化且短（由于测序技术的限制）。宏基因组学数据的复杂性也可能是压倒性的，因为它包含来自不同物种的不同个体的序列（通过随机抽样），或者生活在同一生态位的同一物种的不同菌株。因此，许多有助于许多个体生物基因组计划成功的计算方法并不直接适用于宏基因组学项目。需要开发新的计算方法来优化宏基因组序列数据的分析并推进该领域。叶博士将开发宏基因组序列数据的计算蛋白质功能注释，以改善宏基因组序列数据的功能注释。在该项目中，正在设计和开发软件，通过使用ORF（开放阅读框架）组装和通过专门设计能够容忍测序错误的DNA片段的基因查找器来改进蛋白质序列预测。各种生物学功能，包括生物通路，跨膜转运蛋白和酶的注释正在进行计算工具。正在开发探索性项目，以测试利用宏基因组序列数据来改进功能注释方法的几个想法。专门为宏基因组序列数据分析设计的几种计算工具和管道将作为开放获取发布（例如，与CAMERA合作）。这些工具将通过Ye实验室网站提供：http://mendel.informatics.indiana.edu/~yye/lab/index.phpAs作为她职业生涯奖的一部分，Ye博士将使用宏基因组科学作为教育-研究整合的模式来开发高度整合的活动。PI正在积极与战略指导办公室（OSM），研究生教育和教授计划联盟（AGEP），科学计划中的女性（WISP）和印第安纳州大学的计算（WIC）组织合作，招募学生参加她的计划。

"This award is funded under the American Recovery and Reinvestment Act of 2009(Public Law 111-5)."This is a CAREER award to Dr. Yuzhen Ye of the Department of Informatics at Indiana University. Dr Ye is a second-year tenure track Assistant Professor. Metagenomic sequences are vast in number and as obtained in the lab, fragmented and short (due to the limitations of sequencing techniques). The complexity of metagenomics data can also be overwhelming, as it contains sequences (by random sampling) from different individuals of different species, or different strains of the same species living in the same niche. As a result, many of the computational methods that have contributed to the success of numerous individual organismal genome projects are not directly applicable to metagenomics projects. New computational methods need to be developed to optimize the analysis of metagenomic sequence data and advance the field. This grant to Dr. Ye will develop computational protein function annotation of metagenomic sequence data to improve functional annotation of metagenomic sequence data. In this project, software is being designed and developed for improved protein sequence prediction by using ORF (Open Reading Frame) assembly and by specifically designing a gene finder for DNA fragments that can tolerate sequencing errors. Annotations of various biological functions including biological pathways, transmembrane transporters and enzymes are being carried out with computational tools. Exploratory projects are being developed to test several ideas for utilizing metagenomic sequence data to improve function annotation methods. Several computational tools and pipelines, designed specifically for metagenomic sequence data analysis, will be released as open access (e.g., through collaboration with CAMERA). The tools will be available through the Ye lab website:http://mendel.informatics.indiana.edu/~yye/lab/index.phpAs a part of her CAREER award, Dr. Ye will develop highly-integrated activities using metagenomic science as a model for education-research integration. The PI is actively working with the Office of Strategic Mentoring (OSM), Alliances for Graduate Education and Professoriate Program (AGEP), Women in Science Program (WISP), and Women in Computing (WIC) organizations at Indiana University to recruit students into her program.