BLogo: a tool for visualization of bias in biological sequences

BLogo: a tool for visualization of bias in biological sequences
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BLogo：生物序列偏差可视化工具

DOI：
10.1093/bioinformatics/btn407
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发表时间：
2008-10-01
期刊：
BIOINFORMATICS
影响因子：
5.8
通讯作者：
Wang, Xiaoning
Wang, Xiaoning
中科院分区：
生物学3区
文献类型：
--
作者：
Li, Wencheng;Yang, Bo;Wang, Xiaoning

文献摘要

被引文献

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无标签 Blogo 是一种基于网络的工具，可检测并显示统计上显着的位置特异性序列偏差，同时减少背景噪音。特定位置中被过度代表和未被代表的符号显示在零线上方和下方。当序列处于开放阅读框时，可以针对密码子的三个位置分别计算核苷酸的背景频率，从而大大降低背景噪音。 chi(2) 检验或 Fisher 精确检验用于评估每个位置中每个符号的统计显着性，并且只有那些显着的符号才会在生成的徽标中突出显示。该程序的perl源代码是免费提供的，并且可以在本地运行。 可用性 http://acephpx.cropdb.org/blogo/，http://www.bioinformatics.org/blogo/。
UNLABELLED Blogo is a web-based tool that detects and displays statistically significant position-specific sequence bias with reduced background noise. The over-represented and under-represented symbols in a particular position are shown above and below the zero line. When the sequences are in open reading frames, the background frequency of nucleotides could be calculated separately for the three positions of a codon, thus greatly reducing the background noise. The chi(2)-test or Fisher's exact test is used to evaluate the statistical significance of every symbol in every position and only those that are significant are highlighted in the resulting logo. The perl source code of the program is freely available and can be run locally. AVAILABILITY http://acephpx.cropdb.org/blogo/, http://www.bioinformatics.org/blogo/.