输出位置: 默认值为 meme_out/目录。如果这个目录不存在,会新建一个。输出的文件会有meme.html,meme.xml, meme.txt, meme.xsl以及一些LOGO图片。当然你也可以设置输出的位置。 -o 输出目录名;如果已经存在的话不覆盖该目录; -oc 输出目录名;如...
Meier, J., M€artens, M., Hillebrand, A., Tewarie, P., Van Mieghem, P., 2016a. Motif-based analysis of effective connectivity in brain networks. In: International Workshop on Complex Networks and Their Applications. Springer, pp. 685-696....
MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight ...
(A) Foreground sets in TSMA are defined by differential gene expression analysis of RNA-seq or microarray datasets, usually by selecting statistically significantly upregulated and downregulated genes. The background set is all of the genes in the microarray platform or all of the measured genes in...
* fimo - for scanning sequences with motifs, * mcast - for finding motif clusters, * meme-chip - for analysis of large DNA datasets like ChIPseq output, * spamo - for finding motif complexes by analysing motif spacing, * dreme - for discovery of short regular expression motifs, and that...
Figure 3: K-mer-Based Motif Analysis in Insect Species across Anopheles, Drosophila, and Glossina Genera and Its Application to Species Classification
Arabidopsis thalianaNew motifs for phosphorylation sites associated with calcium-dependent protein kinases were developed using 494 sites experimentally proved in mammalians. Subsequent motif-based search revealed consensus regions in -, -, and -tubulin from Arabidopsis thaliana. The analysis of selected ...
the nodes in the network represent Haiqing Lin's collaborators, and the Network L1 L2 Interlayer motif Motif1 3 Same community2 3 66 ration 1.0 1.0 Interlayer edges Edge3 22 Same community4 20 22 20 Ration5 0.9 0.9 Table 1. Statistical analysis of interlayer edges and motif based ...
203 proteins were identified as DNA-binding transcriptional regulators in the yeast genome [27]. A genome-wide location analysis was carried out for 106 TFs and five NMs were considered significant (auto regulation, feed-forward, single input, multi-input, and regulator cascade). The first four...
Conventional fold recognition techniques rely mainly on the analysis of the entire sequence of a protein. We present an MBA method to improve performance of any conventional sequence-based fold assignment. The method uses sequence motifs, such as those defined in the Prosite database, and the Swis...