MOLECULAR SEQUENCE DATA

分子序列数据

• 批准号: 2901693
• 负责人: SAMUEL KARLIN
• 金额: $ 21.9万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 1988
• 资助国家: 美国
• 起止时间: 1988-08-01 至 2002-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2901693
• 关键词: DNA; analytical method; biochemical evolution; computer assisted sequence analysis; gene expression; genome; mathematical model; nucleic acid sequence; protein sequence; protein structure; statistics /biometry

DESCRIPTION (Adapted from the Investigator's Abstract): The accumulation of molecular sequence data is proceeding at an unprecedented pace. The next phase of molecular biology will be increasingly dominated by efforts to characterize, categorize, and analyze these data with the goal of understanding molecular sequence information and its significance in biological systems. The investigators' proposal is aimed at achieving a deeper understanding of genome structure, function, and evolution using empirical, descriptive and interactive statistical and computational methods. They focus primarily on three interrelated areas: I. Analysis of codon usage patterns. Detailed knowledge of codon and residue choices can help in gene prediction, in characterizing properties of a given gene, and in defining gene classes. They propose a broad analysis of codon usage biases for individual genes and gene classes in complete prokaryotic and eukaryotic genomes. In particular, the investigators' studies will concern codon preferences in different gene classes, including (i) gene classes characterized by function and/or cellular localization; (ii) classes determined by gene size; (iii) codons of a gene divided into three parts: the amino 1/3 part, the middle 1/3 part, and the carboxyl 1/3 part; (iv) genes encoded from the leading vs. lagging strand; and (v) classes of horizontally transferred genes characterized with the aid of codon bias extremes. II. Studies of anomalous genes, including alien genes, highly expressed genes, and those in pathogenicity islands. In complete genomes or in extended contigs of great biological and medical interest are characterizations of alien genes (e.g., laterally transferred), or of alien gene clusters (e.g., pathogenicity or specialization islands), or of highly expressed genes. III. Statistical methods for genome sequence analysis. These will include: (a) characterizations of genomic heterogeneity within and between organisms (e.g., in terms of rare and frequent nucleotides, of motifs, or of compositional biases); (b) extensions of r-scan statistics, which assess anomalies in the distribution of markers along sequences; and (c) statistics of recurrent sequences among genomes characterized by numbers of repeat families, by their sizes (bp or aa.), by spacings between repeats, and by properties of repeat families (intergenic, coding, direct, inverted, mixed).

描述（改编自研究者摘要）： 分子序列数据正在以前所未有的速度进行。下一阶段 分子生物学将越来越多地被表征， 对这些数据进行分类和分析， 序列信息及其在生物系统中的意义。的 研究人员的建议旨在更深入地了解基因组 结构、功能和演变，使用经验性、描述性和互动性 统计和计算方法。主要集中在三个方面 相关领域：一。密码子使用模式分析。的详细知识 密码子和残基的选择可以帮助基因预测， 一个给定的基因的属性，并在定义基因类。他们提出了一个广泛的 个体基因和基因类别的密码子使用偏好分析 完整的原核和真核基因组。特别是，调查人员 研究将关注不同基因类别的密码子偏好，包括 (i)以功能和/或细胞定位为特征的基因类别; (ii)由基因大小决定的类别;（iii）基因的密码子分为三个 部分：氨基1/3部分、中间1/3部分和羧基1/3部分; (iv)由前导链与滞后链编码的基因;和（v） 以密码子偏好性为特征的水平转移基因 极端二.异常基因的研究，包括外来基因， 表达基因和致病岛中的基因。在完整的基因组中， 具有重大生物学和医学意义的延伸重叠群是表征 外来基因（例如，横向转移的），或外来基因簇（例如， 致病性或特化岛），或高表达基因。 三.基因组序列分析的统计方法。这些措施包括： (a)生物体内部和之间的基因组异质性表征 (e.g.,在罕见和常见的核苷酸，基序，或 成分偏差）;（B）r-扫描统计的扩展，其评估 标记物沿着序列分布的异常;以及（c） 以重复家族的数目为特征的基因组中的重复序列， 根据它们的大小（bp或aa.），通过重复之间的间隔，以及 重复家族（基因间、编码、直接、反向、混合）。