OrthReg: a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation

机译：OrthReg：一种基于跨物种直系同源序列保守性预测顺式调控元件的工具

代理获取

本网站仅为用户提供外文OA文献查询和代理获取服务，本网站没有原文。下单后我们将采用程序或人工为您竭诚获取高质量的原文，但由于OA文献来源多样且变更频繁，仍可能出现获取不到、文献不完整或与标题不符等情况，如果获取不到我们将提供退款服务。请知悉。

页面导航

著录项
相似文献
相关主题

著录项

期刊名称 Dong wu xue yan jiu = Zoological Research
作者
Yun-Fei Ma; Cui-Ping Huang; Fang-Ru Lu; Jin-Xiu Li; Xu-Man Han; Adeniyi C. Adeola; Yun Gao; Jia-Kun Deng; Hai-Bing Xie; Ya-Ping Zhang;
展开▼
作者单位

展开▼
年(卷),期 2020(41),4
年度 2020
页码 -1
总页数 5
原文格式 PDF
正文语种
中图分类动物学;
关键词
Comparative genomics;

机译：比较基因组学;

相似文献

外文文献
中文文献
专利

1. BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences [J] . Meng H, Banerjee A, Zhou L Bioinformatics . 2007,第23期

机译：BLISS 2.0：基于Web的工具，可预测远距离直系同源序列中保守的调控模块
2. BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences [J] . Hailong Meng, Arunava Banerjee, Lei Zhou Bioinformatics . 2007,第23期

机译：BLISS 2.0：基于Web的工具，可预测远距离直系同源序列中保守的调控模块
3. BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences [J] . Hailong Meng, Arunava Banerjee, and Lei Zhou Bioinformatics . 2007,第23期

机译：BLISS 2.0：基于Web的工具，可预测远距离直系同源序列中保守的调控模块
4. Cross-species Comparison forIdentifying Orthologous Simple Sequence Repeats of Disease Genes [C] . Chih-Chia Chen, Tsan-Huang Shih, Chien-Ming Chen, Optimization and systems biology . 2009

机译：跨物种比较，确定疾病基因的直系同源序列重复序列
5. Algorithms and tools for cross-species cDNA-to-genome sequence alignment [D] . Zhou, Leming 2008

机译：跨物种cDNA到基因组序列比对的算法和工具
6. BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences [O] . Hailong Meng, Arunava Banerjee, Lei Zhou -1

机译：BLISS 2.0：基于Web的工具可预测远距离直系同源序列中保守的调控模块
7. Figure 4: (A) One conserved sequence, which occurs 79 times in 46,264 binding site peaks from the ChIP-seq data-set. The mutation profile of this conserved sequence is illustrated, where ’_ ’ indicates this base is unchanged; DEL indicates this base is lost; INS X indicates a new base X is inserted in front of this base. (B) Several repeated elements patterns are listed. (C) In the first column, the top five DNA motifs, mined by meme-chip tools (Machanick Bailey, 2011) are illustrated. The resemblant conserved sequences, found by the CFSP algorithm are listed in the second column. In the third column, the position-specific scoring matrices, which are transformed from mutational information are listed. The similarity between meme motif and resemblant conserved sequence with PSSM format was calculated via a stamp motif comparison tool (Mahony Benos, 2007). The E-values for the similarity of those pairs is displayed in the fourth column. (D) One motif is selected in each group clustered by gkmsvm descriptors, and the corresponding motif found by the CFSP algorithm is listed below. (E) There are additional datasets (File No: ENCFF100GRL, ENCFF616IRT, ENCFF870CER, Target: SREBF1) collected from https://www.encodeproject.org. The top two motifs are selected in each file using meme tools, and the corresponding motifs found by our algorithm are listed below. [O] . -1

机译：图4：（a）一种保守序列，其发生在芯片-SEQ数据集中的46,264个结合位点峰值中的79倍。说明了这种保守序列的突变分布，其中'_'表示该碱度不变; del表示此基础丢失; INS X表示新的基础X插入此基础前面。（b）列出了几种重复的元素模式。（c）在第一栏中，示出了由MEME芯片工具（Machanick＆Bailey，2011）开采的前五个DNA主题。由CFSP算法发现的相应保守序列列于第二列中。在第三列中，列出了从突变信息转换的特定位置的评分矩阵。 MEME主题与PSSM格式的相似性与PSSM格式之间的相似性通过邮票图章比较工具（Mahony＆Benos，2007）计算。这些对相似性的电子值显示在第四列中。（d）在由GKMSVM描述符聚集的每个组中选择了一个图案，下面列出了CFSP算法的相应主题。（e）从https://www.encodeproject.org收集的，有附加数据集（文件no：cernff100grl，cenf616irl，conf8.20cer，target：srebf1）。使用MEME工具在每个文件中选择前两个图案，并且我们的算法发现的相应主题如下所示。

OrthReg: a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation

著录项

相似文献

相关主题

期刊订阅