ANALYSIS OF MOLECULAR SEQUENCE DATA

此应用程序请求为我们的研究活动提供支持 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。这个 重点是发展数学、统计和 帮助评估和解释计算概念和方法 分子序列特征。 我们的研究计划将集中在六个主要领域。1) 发展新的统计、评估统计的手段 核苷酸数据表示的意义和方法 和氨基酸序列，可以帮助识别和 解释分子序列关系；2)发展 高效和广泛的计算机算法，用于 识别多个字母之间的重要单词关系 序列；3)密码子和氨基酸性质的研究 关于不同分类的偏好和模式 关于基因；4)对基因的存在或不存在的广泛分析 在许多不同类别的基因上的电荷浓度 功能和结构的种类和可能的解释；5) 寻找构建系统发育树的新途径 偏序准则和共识树的概念；以及6) 包括详细研究的具体比较序列分析 关于(A)多基因家族(珠蛋白、免疫球蛋白)，(B) 疱疹病毒家族尤其是完整的交叉研究 爱泼斯坦-巴尔病毒和水痘带状疱疹病毒基因组，以及(C) 一组逆转录病毒联合的研究， 庚型病毒和转座子元件。 理论分析、数据分析、 计算机算法，以及与生物学家和医学专家的互动 斯坦福大学的教师一直是我们项目的关键因素。这个 我们的团队和成员之间独特的合作 生物和医疗部门提供了理想的框架 实现本基金规定的研究目标。

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.