Software for Analyzing Biosequence Data

用于分析生物序列数据的软件

基本信息

批准号：
7882269
负责人：
Webb Colby Miller
金额：
$ 70.85万
依托单位：
PENNSYLVANIA STATE UNIVERSITY, THE
依托单位国家：
美国
项目类别：
财政年份：
2000
资助国家：
美国
起止时间：
2000-08-15 至 2013-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7882269
关键词：
Acquired Immunodeficiency Syndrome Binding Sites California Chickens Collaborations Communicable Diseases Communities Computer software Computing Methodologies Coupled Cystic Fibrosis Transmembrane Conductance Regulator DNA Sequence Data Data Set Databases Development Elements Environment Evolution Functional RNA Funding GALA Gene Cluster Generations Genes Genetic Genome Genomics Gold Human Human Genome Immunity Individual Influenza Internet Learning Length Macaca mulatta Mammals Methods Modeling Ornithorhynchus anatinus Orthologous Gene Primates Rattus Recording of previous events Regulatory Element Research Running Sequence Alignment Sequence Analysis Shipping Ships Simulate Site System Testing Universities Vertebrates Work Writing base comparative computerized tools design experience genome sequencing improved mouse genome operation programs public health relevance reconstruction software development software systems sound success tool

项目摘要

DESCRIPTION (provided by applicant): The human genome contains several hundred clusters of related genes, in which duplication operations create new gene copies that serve as the raw ingredients for rapid change as humans evolve to adapt to their environment. For instance, many immunity-related genes lie in such clusters. Thus, understanding all of the genetic differences between humans and other primates, or among individual humans, will require a comparative analysis of gene clusters. One benefit will be a better idea of which primate species make the best biomedical models for the progression of infectious diseases like AIDS or influenza in humans. However, the presence of highly similar segments makes it difficult to determine complete and accurate sequence data for these clusters, which has inhibited development of computational methods for their analysis. We propose to collaborate in the generation of accurate primate sequence data for carefully chosen gene clusters, to develop new computational tools for comparative analysis of such data, and to deliver the results to the biomedical community. PUBLIC HEALTH RELEVANCE: Changes within clusters of closely related genes explain many of the differences among humans and primates, as well as among individual humans. We will produce data and computational methods that will greatly increase our understanding of these differences, which may assist with selection of biomedical models for progression of infectious diseases.

描述（由申请人提供）：人类基因组包含数百个相关基因簇，其中重复操作创建了新的基因副本，随着人类的发展以适应其环境，它们是快速变化的原始成分。例如，许多与免疫相关的基因都在此类簇中。因此，了解人类与其他灵长类动物之间或人类之间的所有遗传差异将需要对基因簇进行比较分析。一个好处将是一个更好的想法，即灵长类动物是人类传染病或流感等传染病的发展的最佳生物医学模型。但是，高度相似的细分市场的存在使得很难确定这些簇的完整序列数据，这抑制了计算方法进行分析。我们建议与精心选择的基因簇的准确灵长类动物序列数据合作，开发新的计算工具，以对此类数据进行比较分析，并将结果传递给生物医学群落。公共卫生相关性：密切相关基因群中的变化解释了人类和灵长类动物以及人类之间的许多差异。我们将产生数据和计算方法，从而大大提高我们对这些差异的理解，这可能有助于选择用于传染病进展的生物医学模型。

项目成果

期刊论文数量（53）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Evaluation of methods for detecting conversion events in gene clusters.

检测基因簇中转化事件的方法的评估。

DOI：
10.1186/1471-2105-12-s1-s45
发表时间：
2011
期刊：
BMC bioinformatics
影响因子：
3
作者：
Song,Giltae;Hsu,Chih-Hao;Riemer,Cathy;Miller,Webb
通讯作者：
Miller,Webb

Genomic environment predicts expression patterns on the human inactive X chromosome.

DOI：
10.1371/journal.pgen.0020151
发表时间：
2006-09-29
期刊：
PLoS genetics
影响因子：
4.5
作者：
Carrel L;Park C;Tyekucheva S;Dunn J;Chiaromonte F;Makova KD
通讯作者：
Makova KD

Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species.

选择用于圈养繁殖或重新引入濒危物种的创始个体的优化方法。

DOI：
10.1142/9789814295291_0006
发表时间：
2010
期刊：
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
影响因子：
0
作者：
Miller,Webb;Wright,StephenJ;Zhang,Yu;Schuster,StephanC;Hayes,VanessaM
通讯作者：
Hayes,VanessaM

Revealing mammalian evolutionary relationships by comparative analysis of gene clusters.

DOI：
10.1093/gbe/evs032
发表时间：
2012
期刊：
Genome biology and evolution
影响因子：
3.3
作者：
Song G;Riemer C;Dickins B;Kim HL;Zhang L;Zhang Y;Hsu CH;Hardison RC;Nisc Comparative Sequencing Program;Green ED;Miller W
通讯作者：
Miller W

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.

DOI：
10.1093/nar/gkt911
发表时间：
2014-01
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Giardine B;Borg J;Viennas E;Pavlidis C;Moradkhani K;Joly P;Bartsakoulia M;Riemer C;Miller W;Tzimas G;Wajcman H;Hardison RC;Patrinos GP
通讯作者：
Patrinos GP