MochiView

Application data
Created by	Homann OH and Johnson AD
Biological application domain(s)	Genomics, ChIP-seq, ChIP-on-chip, RNA-Seq, Sequence motifs
Principal bioinformatics method(s)	Genome visualisation, Sequence motif comparison
Created at	University of California at San Francisco
Maintained?	Maybe
Input format(s)	Custom, WIG, BED, GFF, FASTA, MEME, Bioprospector, custom Motif format
Output format(s)	Varied
Software features	Desktop hybrid genome browser and motif visualization/analysis software
Programming language(s)	Java
Operating system(s)	Linux, Mac OS X, Windows

Summary: Hybrid genome browser and motif visualization/analysis/management desktop software.

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MochiView was designed to serve as both a robust genome browser and a motif visualization/analysis platform. It has been used for visualization of Chip-Chip, Chip-Seq, and RNA-Seq data, and it has also been used as a motif-management/analysis database.

Here is a brief summary of some of the MochiView features:

• MochiView is desktop Java software with an integrated database

• MochiView has a rich interface for configuring/saving plot layouts

• The browser has smooth panning/zooming and a very useful data browsing function

• Multiple motif libraries are available on the MochiView website and can be imported directly into the software.

• MochiView contains a large number of motif utilities, including motif comparison, motif position distribution, motif ROC plots, several motif scoring functions, ability to rapidly export motif scoring of location sets or promoters to spreadsheet, etc.

• MochiView also contains Location/Data Set manipulation utilities (e.g. set operations and filters)

• The website contains a tutorial for download that can familiarize you with many of the basic features

• MochiView will write and publish your paper for you. OK, that feature isn't quite ready yet

It is worth noting that MochiView does NOT do "peak-calling" for Chip-Chip or Chip-Seq. MochiView leaves this to the many existing solutions and is more appropriate for downstream visualization and analysis.

Links

• MochiView Homepage [ edit link ]

• Add a Link

References

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