MochiView: versatile software for genome browsing and DNA motif analysis
1 Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
2 Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
BMC Biology 2010, 8:49 doi:10.1186/1741-7007-8-49Published: 21 April 2010
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.
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.
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.