Department of Biochemistry and Biophysics and Program in Molecular Biology and Biotechnology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
Bioinformatics. 2013 Jul 1;29(13):1690-2. doi: 10.1093/bioinformatics/btt264. Epub 2013 May 8.
Many algorithms analyze enhancers for overrepresentation of known and novel motifs, with the goal of identifying binding sites for direct regulators of gene expression. Twine is a Java GUI with multiple graphical representations ('Views') of enhancer alignments that displays motifs, as IUPAC consensus sequences or position frequency matrices, in the context of phylogenetic conservation to facilitate cis-regulatory element discovery. Thresholds of phylogenetic conservation and motif stringency can be altered dynamically to facilitate detailed analysis of enhancer architecture. Views can be exported to vector graphics programs to generate high-quality figures for publication. Twine can be extended via Java plugins to manipulate alignments and analyze sequences.
Twine is freely available as a compiled Java .jar package or Java source code at http://labs.bio.unc.edu/crews/twine/.
Supplementary data are available at Bioinformatics online.
许多算法分析增强子以过度表示已知和新颖的基序,目的是识别基因表达直接调节剂的结合位点。Twine 是一个具有多个图形表示(“视图”)的 Java GUI,可在系统发生保守性的背景下显示基序,例如 IUPAC 共识序列或位置频率矩阵,以促进顺式调控元件的发现。系统发生保守性和基序严格性的阈值可以动态更改,以促进增强子结构的详细分析。视图可以导出到矢量图形程序,以生成用于发布的高质量图。Twine 可以通过 Java 插件进行扩展,以操纵比对和分析序列。
Twine 可作为编译后的 Java.jar 包或 Java 源代码在 http://labs.bio.unc.edu/crews/twine/ 上免费获得。
补充数据可在生物信息学在线获得。