MochiView (''Mo''tif and ''ChI''P ''View''er)
[Homann OR and Johnson AD. MochiView: versatile software for genome browsing and DNA Motif analysis. BMC Biology. 2010, 8:4]
/ref> is software that integrates a genome browser and tools for data and Sequence motif
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''A ...
visualization and analysis. The software uses the Java language, contains a fully integrated JavaDB database, is platform-independent, and is freely available.
Description
MochiView was originally designed as a platform for rapidly browsing, visualizing, and extracting Sequence motif
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''A ...
s from ChIP-chip
ChIP-on-chip (also known as ChIP-chip) is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray (''"chip"''). Like regular Ch-IP, ChIP, ChIP-on-chip is used to investigate interactions between proteins and DNA ''in ...
and ChIP-Seq
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with Massively parallel signature sequencing, massively parallel DNA sequencing to identify t ...
data. The software uses a generalized data format that serves other purposes as well, such as the visualization and analysis of RNA-Seq
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also k ...
data or the import, maintenance, exploration, and analysis of Sequence motif
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''A ...
libraries. The MochiView website[{{Cite web , url=http://johnsonlab.ucsf.edu/sj/mochiview-screenshots/ , title=MochiView website: sample videos , access-date=2010-05-12 , archive-url=https://web.archive.org/web/20100813111924/http://johnsonlab.ucsf.edu/sj/mochiview-screenshots/ , archive-date=2010-08-13 , url-status=dead ] of the software showing smooth panning/zooming, data/gene/sequence/coordinate browsers, and plot interactivity. The software was created by Oliver Homann in the laboratory of Alexander Johnson at the University of California at San Francisco.
References
External links
* MochiView websit
Bioinformatics software