diChIPMunk

[…] ndencies have been shown to outperform simpler motif models like the PWM model [–]. Examples for highly popular tools that model intra-motif dependencies are Dimont [], MEME-ChIP [], DeepBind [], and diChIPMunk [].In contrast, the second group of de-novo motif discovery approaches known as phylogenetic footprinting incorporates orthologous sequences of at least two phylogenetically related species […]

[…] as done using MACS2 () (https://github.com/taoliu/MACS) against preimmune and input control data. Peak sets obtained with the preimmune control were smaller and were utilized for motif discovery with diChIPMunk (,). Resulting dinucleotide position weight matrices were used for motif finding in peaks obtained with the input control. To detect peaks with strong motif occurrences, we estimated a P-va […]

[…] e of pattern matching and pattern detection approaches for TFBS prediction in the context of ChIP-Seq data, we applied oPWM and SiteGA (as representatives of the former class) as well as ChIPMunk and diChIPMunk (as representatives of the latter class) to analyze a dataset of 4455 FoxA2-binding loci (ChIP-Seq peaks with read coverage of at least 15) in mouse adult liver chromatin [].To produce a su […]

[…] otif order 1 than for motif order 0 for at least one combination of training and test data sets in Supplementary Figure S5–S13, and we compare the dependencies detected by Dimont to those detected by diChIPMunk () in Section 6 of the Supplementary Material. […]