MochiView: versatile software for genome browsing and DNA motif analysis

Abstract

Background: As high-throughput technologies rapidly generate genome-scale data, it becomes increasingly important to visually integrate these data so that specific hypotheses can be formulated and tested.

Results: We present MochiView, a platform-independent Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis in a visually-appealing and user-friendly application.

Conclusions: While highly versatile, the software is particularly useful for organizing, exploring, and analyzing large genomic data sets, such as those from deep RNA sequencing, chromatin immunoprecipitation experiments (ChIP-Seq and ChIP-Chip), and transcriptional profiling. MochiView provides an extensive suite of utilities to identify and to explore connections between these data sets and short sequence motifs present in DNA or RNA.

Figure 1

A sample MochiView screenshot, demonstrating many of the available display formats. A 20 kb span of the Candida albicans genome is displayed. (a) Two line graphs utilizing the same y-axis and representing experimental (red) and control (blue) ChIP-chip enrichment data for the Zap1 transcription factor [33]. (b) A gene track, including color-coded data representing log₂-transformed expression values from a microarray experiment. This experiment compares a wild-type strain to a Zap1 deletion strain. Note that red indicates the highest expression change; ZRT2 is likely to be a direct target of Zap1. Gene tracks can also display genes containing multiple isoforms and coding- and non-coding exons (not shown). (c) A bar graph track, demonstrating an alternate means of displaying the experimental ChIP-chip data represented by the red line graph in (A). (d) A region marker track, depicting a ChIP binding region and -log₁₀-transformed P-value. (e) An RNA sequencing track, depicting mock data mapped to the plus strand (blue) and minus strand (orange). (f) A motif track, depicting the motif match scores of instances of four different DNA motifs, each assigned to a different color. (g) A multiple genome alignment track (several species of yeast), shaded to represent the level of conservation. (h) A line graph track, representing the GC-content of the DNA. (i) The data browser, which displays the contents of the database in an interactive table. Clicking on a row in the table centers the plot on the corresponding region. (j) Additional features become evident as the plot is zoomed in. Shown here are close-ups of the motif and alignment tracks (F and G, respectively).

Figure 2

An overview of MochiView's regulatory motif analysis and management tools. (a) MochiView provides a simple interface for browsing and annotating a motif library. (b) MochiView provides numerous utilities for importing and exporting motif frequency matrices and logos, including support for motifs based on degenerate DNA sequences, frequency matrices, or affinity matrices (as produced by the program MatrixREDUCE [7]). (c) MochiView contains a motif detection utility that can identify de novo motifs enriched in user-defined regions. (d) A motif comparison tool identifies similarities between newly discovered motifs and those in the motif library. (e) Two utilities are provided for analyzing motif enrichment in sets of user-defined regions. (f) Utilities are provided for detecting non-random distribution of motifs relative to either a set of user-defined locations (for example, start codons or peaks of ChIP enrichment) or strong instances of another motif (for example, co-occurring motifs that are typically separated by a 25 bp gap). (g) Several utilities are provided for scoring motifs against user-defined regions. For example, it is relatively simple to output a file containing the top motif score upstream of each gene for every motif in the library. (h) Enrichment for Gene Ontology terms can be determined for genes with upstream sequence that contains a strong instance of a motif.