De novo assembly software tools | ChIP sequencing data analysis
The ability to perform de novo-based analysis of ChIP-Seq data opens the door to several possibilities. These include: (1) comparison of binding motifs for mutated versus wild-type transcription factors; and (2) motif evolution analysis in developmental studies, for species that have not been fully sequenced. It also enables researchers to analyze data from studies in which we may expect the genome being analyzed to diverge from the reference genome for that species.
A computational pipeline to extract the transcription factor binding motifs from ChIP-seq data, assuming no reference genome is available. denovochipseq combines de novo assembly with statistical tests enabling motif discovery without the use of a reference genome. We validate the performance of denovochipseq using human and mouse data. Analysis of fly data indicates that denovochipseq outperforms alignment based methods that utilize closely related species.
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