ANALYSIS OF MOLECULAR SEQUENCE DATA

本申请请求支持我们的研究活动 关注识别和分类模式的问题 在核酸和蛋白质序列内和之间。 的 重点是发展数学，统计和 计算概念和方法，以帮助评估和解释 分子序列特征 我们的研究计划将集中在六个主要领域。 第一章 发展新的统计数据，评估统计数据的手段 核苷酸数据表示意义和方法 和氨基酸序列，其可以帮助鉴定和 解释分子序列关系; 2）开发 有效和广泛的计算机算法， 识别多个字母之间重要单词关系 密码子和氨基酸性质的研究 不同分类的偏好和模式 4）广泛分析基因的存在或不存在 电荷浓度超过不同类别的基因在许多 物种和功能和结构的可能解释; 5） 追求新的方法，系统发育建设， 共识树的偏序准则和概念;以及6） 特定的比较序列分析，包括详细的研究 （a）多基因家族（球蛋白，免疫球蛋白），（B） 疱疹病毒家族特别是交叉研究的完整 爱泼斯坦巴尔病毒和水痘带状疱疹病毒基因组，和（c） 研究一组逆转录病毒的结合， 嗜肝病毒和转座子元件。 理论分析，数据分析， 计算机算法，以及与生物学家和医学 斯坦福大学的教师一直是我们项目的关键因素。 的 我们的团队和成员之间的独特合作 生物学和医学部门提供了一个理想的框架， 实现本补助金规定的研究目标。

This application requests support for our research activities concerned with problems of identifying and classifying patterns within and between nucleic acid and protein sequences. The emphasis is on developing mathematical, statistical and computing concepts and methods to help assess and interpret molecular sequence features. Our research program will concentrate in six main areas. 1) Development of new statistics, means for assessing statistical significance, and methods of data representations for nucleotide and amino acid sequences that can aid in identifying and interpreting molecular sequence relationships; 2) development of efficient and wide-ranging computer algorithms by which to identify significant word relationships among multiple letter sequences; 3) investigation of the nature of codon and amino acid preferences and patterns with respect to different classifications of genes; 4) extensive analysis of the presence or absence of charge concentrations over different categories of genes in many species and possible interpretations for function and structure; 5) pursuit of new approaches for phylogenetic constructions using partial ordering criteria and concepts of consensus trees; and 6) specific comparative sequence analyses to include detailed studies on (a) multigene families (globins, immunoglobulins), (b) the Herpes virus family especially cross studies of the complete Epstein Barr virus and the Varicello Zoster virus genomes, and (c) investigation of the conjunction of a set of retroviruses, hepadnoviruses, and transposon elements. The interplay between theoretical analysis, data analysis, computer algorithms, and interaction with biologists and medical faculty at Stanford has been a key factor in our program. The unique collaboration between our group and members of the biology and medical departments provides an ideal framework for achieving the research objectives defined in this grant.