A CRITICAL EVALUATION AND COMPARISON OF COMPUTERIZED SEQUENCE ANALYSIS SYSTEMS

计算机化序列分析系统的批判性评估和比较

• 批准号: 3774931
• 负责人: M J MILLER
• 金额: --
• 依托单位: DIVISION OF CANCER EPIDEMIOLOGY AND GENETICS
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/3774931
• 关键词: DNA; computer assisted sequence analysis; computer program /software; computer system design /evaluation; nucleic acid sequence

In collaboration with the BioInfomatics and Molecular Analysis Section (BIMAS) at the Division of Computer Research and Technology, we are engaged in a critical, quantitative comparison of several computer programs designed for gene sequence assembly and analysis. The aim of this study was to gain experience and expertise in the use of several different sequence assembly programs, and to evaluate these programs as to their speed, accuracy, and ease of use. Six sequence assembly packages have been examined: the "Inherit" System (Applied Biosystems); GCG (Genetics Computer Group); Sequencher 2.0 (Gene Codes Co.); GeneWorks (Intelli-Genetics); SeqMan (DNAStar); and AssemblyLING (International Biotechnologies). Inherit makes heavy use of a specialized parallel processing computer capable of scanning and comparing over 15 million characters per second. Inherit is primarily designed for assembly of medium to large sequencing projects, for searching the gene and protein databases for homologous gene sequences, and to quickly search for genetic motifs such as regulatory elements. Unfortunately, much of the Inherit software is bug ridden, and poorly designed. To evaluate the speed and quality of sequence assembly, the rat multidrug resistance gene sequence was randomly split into 58 overlapping fragments. From 0 to 15% error was randomly added to different sets of these fragments. The Inherit and GCG programs gave the best final assemblage results. At 5% added error approximately 50 bases were at variance from the final sequence (1% error). The Sequencher and SeqMan programs consistently gave two to three times as much apparent error. However, the Sequencher program has a contig editing system that is an order of magnitude superior to any of the other editors. Two programs gave unacceptable results. At 5% added error, both AssemblyLING and GeneWorks had between 900 and 1000 variant bases (20% error). GeneWorks frequently misaligned the fragments, even if there was no error added to them.

与生物信息学和分子分析科合作 （BIMAS）在计算机研究和技术部门，我们是 对几台计算机进行了严格的定量比较， 用于基因序列组装和分析的程序。 的目的 这项研究是为了获得经验和专业知识，在使用几个 不同的序列组装程序，并评估这些程序， 他们的速度，准确性和易用性。 六个序列组装包 已被检查：“继承”系统（应用生物系统）; GCG （Genetics Computer Group）; Sequencher 2.0（Gene Codes Co.）; GeneWorks （智能遗传学）; SeqMan（DNAStar）;和汇编（国际 生物技术）。 Inherit大量使用专门的并行 处理计算机能够扫描和比较超过1500万 字符/秒。 Inherit主要设计用于 中型到大型测序项目，用于搜索基因和蛋白质 同源基因序列的数据库，并快速搜索遗传 例如调控元件。 不幸的是， 软件是错误缠身，设计拙劣。 为了评估速度和 序列组装质量，大鼠多药耐药基因序列 随机分成58个重叠片段。 从0到15%的误差是 随机添加到这些片段的不同集合中。 继承和GCG 程序给出了最好的最终装配结果。 在5%的附加误差下 大约50个碱基与最终序列有差异（1%）， 错误）。 Sequencher和SeqMan程序始终给出2到3个 倍的明显错误。 然而，Sequencher程序具有 叠连群编辑系统，其是优于任何一个的数量级上级。 其他编辑。 有两个项目的结果令人无法接受。 添加5% 错误，AssemblyLING和GeneWorks都有900到1000个变体 误差（20%）。 基因工程经常使片段错位，即使 没有任何错误添加到它们中。