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Figure 1 | BMC Biology

Figure 1

From: MochiView: versatile software for genome browsing and DNA motif analysis

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).

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