The MEME suite of motif-based sequence analysis tools

基于基序的序列分析工具 MEME 套件

• 批准号: 8129528
• 负责人: William Stafford Noble
• 金额: $ 32.59万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-28 至 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8129528
• 关键词: Accounting; Active Sites; Algorithms; Amino Acid Motifs; Amino Acid Sequence; Architecture; Back; Base Sequence; Binding Sites; Biological; Biological Assay; Biological Process; Biology; Cell physiology; Cells; Code; Collection; Communities; Complement; Complex; Computer software; Cues; DNA; DNA Sequence; Data; Data Files; Data Set; Databases; Development; Disease; Disease model; Documentation; Elements; Engineering; Enzymes; Epigenetic Process; Extensible Markup Language; Family member; Funding; Genes; Genetic Transcription; Genome; Genomics; Goals; Grant; Health; Individual; Internet; Investments; Knowledge; Maintenance; Methylation; Modeling; Molecular; Molecular Evolution; Names; Nuclear; Nucleosomes; Online Systems; Output; Pattern; Peptide Sequence Determination; Phase; Philosophy; Phylogenetic Analysis; Positioning Attribute; Process; Property; Protein Binding; Protein Family; Proteins; Protocols documentation; Resource Allocation; Resources; Scanning; Scientist; Sequence Analysis; Series; Services; Signal Transduction; Site; Software Engineering; Software Tools; Source; Statistical Models; Update; Work; base; biological research; data format; design; detector; genome-wide; histone modification; human disease; improved; interoperability; molecular scale; novel; programs; protein folding; response; tool; transcription factor; usability; user-friendly; web based interface; web interface; web services

DESCRIPTION (provided by applicant): DNA and protein sequences digitally store information about biological function in a complex code that is not yet fully understood. The fundamental unit of this code is the sequence motif, which is defined as a small, recurring DNA or protein sequence pattern. A DNA motif might be involved, for example, in turning on or off the transcription of a gene in response to environmental cues. A protein motif might encode the properties of the binding site that allows the protein to carry out its function. The MEME Suite of motif-based sequence analysis software builds statistical models of DNA and protein motifs, allowing biologists to discover novel motifs, to search for new instances of known motifs, and to compare motifs to one another. This proposal continues to develop and maintain the MEME Suite, which is in regular use by biologists around the world. The aims of this work are five-fold: (1) to increase the accessibility, usability and interoperability of the MEME Suite, (2) to expand the MEME Suite to handle epigenetic data regarding histone modifications, methylation, nucleosome positioning and DNaseI hypersensitive sites, (3) to integrate a variety of existing motif-based software tools into the MEME Suite, (4) to augment the algorithms used by the MEME Suite with proven enhancements, and (5) to continue to improve our user support services. PUBLIC HEALTH RELEVANCE: This project will improve existing, widely used software that enables biologists to understand how DNA and protein sequences encode information about biological function. Identifying and accurately characterizing functional sequence motifs allows scientists to understand how genes are turned on and off and how proteins carry out their functions in the cell. Such knowledge is fundamental to any model of the basic molecular mechanisms of the cell, and in particular, for molecular-scale models of disease processes.

描述（由申请人提供）：DNA和蛋白质序列以复杂的密码数字化存储有关生物功能的信息，但尚未完全理解。这个密码的基本单位是序列基序，它被定义为一个小的，重复的DNA或蛋白质序列模式。例如，DNA基序可能参与响应环境线索开启或关闭基因转录。蛋白质基序可能编码允许蛋白质执行其功能的结合位点的特性。基于基序的序列分析软件MEME Suite构建了DNA和蛋白质基序的统计模型，使生物学家能够发现新的基序，搜索已知基序的新实例，并将基序相互比较。该提案继续开发和维护MEME套件，该套件由世界各地的生物学家定期使用。这项工作的目标有五个方面：（1）增加MEME套件的可访问性、可用性和互操作性，（2）扩展MEME套件以处理关于组蛋白修饰、甲基化、核小体定位和DNaseI超敏位点的表观遗传数据，（3）将各种现有的基于基序的软件工具整合到MEME套件中，（4）通过经验证的增强功能来增强MEME套件所使用的算法，以及（5）继续改进我们的用户支持服务。公共卫生相关性：该项目将改进现有的广泛使用的软件，使生物学家能够了解DNA和蛋白质序列如何编码有关生物功能的信息。识别和准确表征功能序列基序使科学家能够了解基因如何打开和关闭以及蛋白质如何在细胞中发挥功能。这些知识对于细胞基本分子机制的任何模型，特别是对于疾病过程的分子尺度模型都是至关重要的。

项目成果

An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation.

• DOI: 10.1186/1471-2164-15-231
• 发表时间: 2014-03-25
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Lajoie M;Hsu YC;Gronostajski RM;Bailey TL
• 通讯作者: Bailey TL

Inferring transcription factor complexes from ChIP-seq data.

• DOI: 10.1093/nar/gkr341
• 发表时间: 2011-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Whitington T;Frith MC;Johnson J;Bailey TL
• 通讯作者: Bailey TL

STREAM: Static Thermodynamic REgulAtory Model of transcription.

• DOI: 10.1093/bioinformatics/btn467
• 发表时间: 2008-11-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Bauer DC;Bailey TL
• 通讯作者: Bailey TL

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.

• DOI: 10.1186/1471-2105-8-385
• 发表时间: 2007-10-15
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Redhead E;Bailey TL
• 通讯作者: Bailey TL

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation.

• DOI: 10.1093/nar/gku801
• 发表时间: 2014
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: O'Connor TR;Bailey TL
• 通讯作者: Bailey TL