Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.
Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.
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DOI：
10.1093/nar/gks469
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发表时间：
2012-07
影响因子：
14.9
通讯作者：
Nielsen M
中科院分区：
文献类型：
--
作者：
Thomsen MC;Nielsen M
Seq 2 Logo是一个基于Web的序列徽标生成器。序列标志是存储在多序列比对（MSA）中的信息内容的图形表示，并且提供生物序列中结合基序、活性位点等的位置特异性氨基酸组成的紧凑且高度直观的表示。序列标志的准确生成通常受到序列冗余和低观测数量的影响。此外，大多数可用于序列标识生成的方法集中于显示氨基酸的位置特异性富集，丢弃了与氨基酸缺失相关的同等有价值的信息。Seq 2logo旨在解决这些问题，允许用户包括序列加权以校正数据冗余，伪计数以校正低数量的观察结果和不同的标识表示，每个标识表示捕获与氨基酸富集和耗尽相关的不同方面。除了允许以肽和MSA的形式输入外，Seq 2Logo还接受Blast序列特征的输入，为非专业的最终用户提供了方便的访问，以表征和鉴定任何给定的感兴趣蛋白质中的功能保守/可变氨基酸。服务器的输出是序列徽标和PSSM。Seq 2Logo可在http://www.cbs.dtu.dk/biotools/Seq2Logo上获得（2012年5月14日，最后访问日期）。
Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed).
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
--
作者：
SHANNON, CE
通讯作者：
SHANNON, CE
影响因子：
--
作者：
KULLBACK, S;LEIBLER, RA
通讯作者：
LEIBLER, RA
Enologos：用于能量归一化序列徽标的多功能网络工具。
影响因子：
14.9
作者：
Workman, CT;Yin, YT;Corcoran, DL;Ideker, T;Stormo, GD;Benos, PV
通讯作者：
Benos, PV
影响因子：
5.8
作者：
Vacic, Vladimir;Iakoucheva, Lilia M.;Radivojac, Predrag
通讯作者：
Radivojac, Predrag