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Chipster is a user-friendly analysis software for high-throughput data. It contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.
When the protein is a transcription factor, the enriched area is its transcription factor binding site (TFBS). Popular software programs include MACS. [2] Wilbanks and colleagues [3] is a survey of the ChIP-seq peak callers, and Bailey et al. [4] is a description of practical guidelines for peak calling in ChIP-seq data.
Central Motif Enrichment Analysis (CentriMo) is a tool for inferring direct DNA binding from ChIP-seq data. CentriMo is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ChIP-seq peak regions. CentriMo takes a ...
Schematic overview of the modular structure underlying procedures for gene set enrichment analysis. Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g ...
SMiLE-seq workflow. SMiLE-seq uses a microfluidic device into which transcription factors, which have been transcribed and translated in vitro, are loaded.Transcription factor samples (~0.3 ng) are modified by the addition of an enhanced green fluorescent protein (eGFP) tag and combined with both target double-stranded DNA molecules (~8 pmol) tagged with Cyanine Dye5 (Cy5) and a double ...
Graphical analysis tool to find all open reading frames: Prokaryotes, Eukaryotes [40] Regulatory Sequence Analysis Tools: Series of modular computer programs to detect regulatory signals in non-coding sequences: Fungi, Prokaryotes, Metazoa, Protist, Plants [41] [42] PHANOTATE: A tool to annotate phage genomes. Phages [43] SplicePredictor