What is MochiView?

MochiView is Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis.  It is a pure Java desktop application that is easy to use and that can produce data and plots that are easily exportable for publication
or analysis with other programs.  Download here.

What kinds of data can be viewed in MochiView?

  • ChIP-Seq
  • RNA-Seq
  • DNA binding motifs
  • ChIP-chip
  • Multiple genome alignments   
  • Expression data
  • Any data consisting of DNA-sequence positional information

How does MochiView display this data?

MochiView provides a powerful interface for setting up plots using anything loaded into the database.  Data can be displayed in a variety of formats, including line graphs, bar graphs, shapes, and the color and appearance of these formats is customizable.

A sample plot is shown below with (from top to bottom) ChIP-Seq data, annotated genes, motif scores for motif 1, motif scores for motif 2, and RNA-Seq counts for plus and minus strands in two conditions. 

Navigating MochiView

MochiView provides powerful search and navigation tools to make data browsing easy, including:

  • Sort data sets by value to move between areas of interest (such as highly-expressed genes)
  • Search by gene name
  • Search for sequences or palindromes

Motifs in MochiView

MochiView provides a convenient interface for maintaining, viewing, and annotating a motif library.  Motifs can be imported in multiple formats, and several pre-compiled motif libraries are also available on the Downloads page. In addition, MochiView provides multiple tools for various motif analyses including:

  • Motif scoring (with several scoring options)
  • Integrated de novo motif finder
  • Motif Enrichment analysis (including ROC plots)
  • Motif comparison utility
  • Motif distribution utilities
  • Motif GO enrichment
  • Export visually appealing motif logos

Data Analysis in MochiView

Many other types of data analysis are possible in MochiView including:

  • Extract enriched regions from ChIP-Seq data
  • Map ChIP-Seq data onto regions of interest
  • Combine/manipulate ChIP-Seq and RNA-Seq data sets
  • Filter your data and location sets
  • Smooth data for display
  • Extract peaks from data
  • Annotation locations with proximal genes
  • GO Enrichment analysis
  • Build a promoter set 

Downloading MochiView

Download here