MACSIMS: multiple alignment of complete sequences information management system.
MACSIMS: multiple alignment of complete sequences information management system.
复制标题
DOI：
10.1186/1471-2105-7-318
复制
发表时间：
2006-06-23
影响因子：
3
通讯作者：
Poch O
中科院分区：
文献类型：
--
作者：
Thompson JD;Muller A;Waterhouse A;Procter J;Barton GJ;Plewniak F;Poch O
在后基因组时代，正在进行系统级研究，试图通过整合来自基因组学、蛋白质组学或转录组学等领域的各种资源来解释复杂的生物系统。现在需要新的信息管理系统来收集、验证和分析大量的不同种类的数据。完整序列的多重比对为在蛋白质家族的背景下整合这些信息提供了理想的环境。MACSIMS是一个基于多重测序的信息管理程序，它结合了基于知识和从头算序列分析方法的优点。结构和功能信息从公共数据库自动检索。在多重比对中，同源区域被鉴定，并且检索的数据被评估，并且从已知序列传播到具有这些可靠区域的未知序列。在大规模评估中，传播的序列特征的特异性估计为> 99%，即做出非常少的假阳性预测。然后，MACSIMS被用来检测已知与人类遗传疾病有关的100种蛋白质的测试集的突变。与公共数据库中可用的特征相比，与这些蛋白质相关的序列特征的数量增加了60%。XML格式的输出文件允许自动解析MACSIM结果，而使用JalView程序的图形显示允许手动分析。MACSIMS是一个新的信息管理系统，它结合了蛋白质家族在结构，功能和进化水平上的详细分析。因此，MACSIMS提供了一个独特的环境，便于知识提取和最相关的信息，以生物学家的介绍。Web服务器和源代码可在.
In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at .
登录
查看更多内容
影响因子：
4.3
作者：
Engelhardt BE;Jordan MI;Muratore KE;Brenner SE
通讯作者：
Brenner SE
影响因子：
8
作者：
King, RD;Sternberg, MJE
通讯作者：
Sternberg, MJE
影响因子：
3
作者：
Koski LB;Gray MW;Lang BF;Burger G
通讯作者：
Burger G
影响因子：
5.8
作者：
Frenkel-Morgenstern, M;Voet, H;Pietrokovski, S
通讯作者：
Pietrokovski, S
影响因子：
14.9
作者：
Katoh, K;Misawa, K;Miyata, T
通讯作者：
Miyata, T