Mulan: multiple-sequence alignment to predict functional elements in genomic sequences.
Mulan: multiple-sequence alignment to predict functional elements in genomic sequences.
复制标题
DOI：
10.1007/978-1-59745-514-5_15
复制
发表时间：
2007
影响因子：
--
通讯作者：
G. Loots;I. Ovcharenko
中科院分区：
文献类型：
--
作者：
G. Loots;I. Ovcharenko
多序列比对分析是将进化选择能力转化为系统发育关系以定位功能编码和非编码基因组元件的有效方法。木兰工具(http://mulan.dcode.org/)被设计成有效地对基因组序列进行多重比较，这是促进生物信息驱动的生物发现所必需的。木兰网络服务器能够比较近亲和远亲的基因组，以确定在广泛的进化时间范围内的保守元件。在该工具中结合了几种新的算法：用于快速识别局部序列保守性的TBA多序列比对程序和用于在比对中检测进化保守的转录因子结合位点的多TF程序。木兰与ERC浏览器集成，UCSC基因组浏览器用于快速上传可用序列，并支持与GALA数据库的双向通信，以使用序列保守简档覆盖GALA功能基因组注释。木兰计算的局部多重比对确保了远程生物体中短期和大规模基因组重排的可靠表示。最近，我们还引入了处理复制的能力，以允许可靠地重建作为基因组序列数据基础的进化事件。在这里，我们描述了木兰工具的主要功能，包括交互修改关键的保守参数，可视化选项，以及从可视化图形动态访问序列数据，以灵活和易于执行的分析差异进化的基因组区域。
Multiple sequence alignment analysis is a powerful approach for translating the evolutionary selective power into phylogenetic relationships to localize functional coding and noncoding genomic elements. The tool Mulan ( http://mulan.dcode.org/ ) has been designed to effectively perform multiple comparisons of genomic sequences necessary to facilitate bioinformatic-driven biological discoveries. The Mulan network server is capable of comparing both closely and distantly related genomes to identify conserved elements over a broad range of evolutionary time. Several novel algorithms are brought together in this tool: the tba multisequence aligner program used to rapidly identify local sequence conservation and the multiTF program to detect evolutionarily conserved transcription factor binding sites in alignments. Mulan is integrated with the ERC Browser, the UCSC Genome Browser for quick uploads of available sequences and supports two-way communication with the GALA database to overlay GALA functional genome annotation with sequence conservation profiles. Local multiple alignments computed by Mulan ensure reliable representation of short- and large-scale genomic rearrangements in distant organisms. Recently, we have also introduced the ability to handle duplications to permit the reliable reconstruction of evolutionary events that underlie the genome sequence data. Here, we describe the main features of the Mulan tool that include the interactive modification of critical conservation parameters, visualization options, and dynamic access to sequence data from visual graphs for flexible and easy-to-perform analysis of differentially evolving genomic regions.