Gordon D Benjamin, Nekludova Lena, McCallum Scott, Fraenkel Ernest
Whitehead Institute for Biomedical Research, Nine Cambridge Center Cambridge, MA 02142, USA.
Bioinformatics. 2005 Jul 15;21(14):3164-5. doi: 10.1093/bioinformatics/bti481. Epub 2005 May 19.
TAMO (Tools for Analysis of MOtifs) is an object-oriented computational framework for interpreting transcriptional regulation using DNA-sequence motifs. To simplify the application of multiple motif discovery programs to genome-wide data, TAMO provides a sophisticated motif object with interfaces to several popular programs. In addition, TAMO provides modules for integrating motif analysis with diverse data sources including genomic sequences, microarrays and various databases. Finally, TAMO includes tools for sequence analysis, algorithms for scoring, comparing and clustering motifs, and several useful statistical tests. Recently, we have applied these tools to analyze tens of thousands of motifs derived from hundreds of microarray experiments.
TAMO（基序分析工具）是一个面向对象的计算框架，用于利用DNA序列基序解释转录调控。为了简化将多个基序发现程序应用于全基因组数据的过程，TAMO提供了一个复杂的基序对象，并带有与几个流行程序的接口。此外，TAMO还提供了用于将基序分析与包括基因组序列、微阵列和各种数据库在内的多种数据源进行整合的模块。最后，TAMO包括序列分析工具、基序评分、比较和聚类算法，以及一些有用的统计测试。最近，我们已应用这些工具来分析从数百个微阵列实验中获得的数以万计的基序。
