使用Galaxy、Table Browser和GALA从多物种比对中对顺式调控模块进行计算预测。

Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA.

作者信息

Elnitski Laura, King David, Hardison Ross C

机构信息

Genome Technology Branch, National Institutes of Health, Rockville, MD, USA.

出版信息

Methods Mol Biol. 2006;338:91-103. doi: 10.1385/1-59745-097-9:91.

DOI:10.1385/1-59745-097-9:91

PMID:16888352

Abstract

One major goal of genomics is to identify all the functional sequences in genomes, including sequences that regulate the expression of genes. Sequence conservation is a good, albeit imperfect, guide to these functional elements. We describe how to use publicly available servers (Galaxy, the UCSC Table Browser, and GALA) to find genomic sequences whose alignments (from blastZ and multiZ) show properties associated with cis-regulatory modules, such as high conservation score, high regulatory potential score, and conserved transcription factor binding sites. Links to these servers can be accessed at http://www.bx.psu.edu/ and http://genome.ucsc.edu/.

摘要

基因组学的一个主要目标是识别基因组中的所有功能序列，包括调控基因表达的序列。序列保守性是这些功能元件的一个良好但并不完美的指引。我们描述了如何使用公开可用的服务器（Galaxy、加州大学圣克鲁兹分校表浏览器和GALA）来查找其比对结果（来自blastZ和multiZ）显示出与顺式调控模块相关特性的基因组序列，例如高保守得分、高调控潜力得分以及保守的转录因子结合位点。可通过http://www.bx.psu.edu/和http://genome.ucsc.edu/访问这些服务器的链接。