A DNA SEQUENCE ASSEMBLY PROGRAM

DNA 序列组装程序

• 批准号: 6637425
• 负责人: Xiaoqiu Huang
• 金额: $ 14.07万
• 依托单位: IOWA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 1996
• 资助国家: 美国
• 起止时间: 1996-08-01 至 2004-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6637425
• 关键词: DNA; biotechnology; computer assisted sequence analysis; computer program /software; computer system design /evaluation; nucleic acid repetitive sequence; nucleic acid sequence; parallel processing

DESCRIPTION (Adapted from the Investigator's Abstract): The investigators will develop and improve a DNA sequence assembly program for supporting large-scale DNA sequencing projects at public-funded genome centers. They developed a sequence assembly program named CAP3 in the initial project period. They propose to add new capabilities and make improvements to the CAP3 program. Specifically, the investigators will (1) improve the method for using forward-reverse constraints, (2) improve the method for generating consensus sequences, (3) add an option to support directed assembly in the sequence finishing phase, (4) add a capability to use databases of protein and EST sequences to order contigs produced in low-pass sequencing projects, and (5) add a capability to address alternative splicing patterns in assembly of EST sequences. They will work closely with Dr. Lee Hood's genome center. This relationship will ensure that their efforts on the assembly program will be relevant to real-world sequencing projects. The investigators will also assist the integration of their assembly program into sequencing environments at other genome centers.

描述（改编自研究者摘要）：研究者将 开发和改进DNA序列组装程序，以支持大规模的 公共资助的基因组中心的DNA测序项目。他们开发了一种 在项目初期，我们开发了一个名为CAP 3的序列组装程序。他们 建议增加新的能力，并对CAP 3计划进行改进。 具体而言，研究人员将（1）改进使用方法 正向-反向约束，（2）改进共识生成方法 序列，（3）添加选项以支持序列中的定向组装 完成阶段，（4）增加使用蛋白质和EST数据库的能力 对低通测序项目中产生的重叠群进行排序的序列，以及（5） 在EST组装中增加解决可变剪接模式的能力 序列的他们将与李·胡德博士的基因组中心密切合作。这 这种关系将确保他们在组装计划上的努力将得到 与现实世界的测序项目相关。调查人员还将协助 将他们的组装程序整合到测序环境中， 基因组中心

项目成果

MAP2: multiple alignment of syntenic genomic sequences.

MAP2：同线性基因组序列的多重比对。

• DOI: 10.1093/nar/gki159
• 发表时间: 2005
• 期刊: Nucleic acids research.
• 作者: Ye,Liang;Huang,Xiaoqiu
• 通讯作者: Huang,Xiaoqiu

A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage.

一种在深度覆盖序列中查找具有等位基因频率的单核苷酸多态性的方法。

• DOI: 10.1186/1471-2105-6-220
• 发表时间: 2005
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Wang,Jianmin;Huang,Xiaoqiu
• 通讯作者: Huang,Xiaoqiu

MAVG: locating non-overlapping maximum average segments in a given sequence.

MAVG：在给定序列中定位不重叠的最大平均段。

• DOI: 10.1093/bioinformatics/19.1.151
• 发表时间: 2003
• 期刊: Bioinformatics (Oxford, England)
• 作者: Lin,Yaw-Ling;Huang,Xiaoqiu;Jiang,Tao;Chao,Kun-Mao
• 通讯作者: Chao,Kun-Mao