Hope you don't mind my posting a plug for my software here ... hopefully some of you will find it useful. I've written a desktop java software application called MochiView that is a hybrid genome browser and motif analysis/visualization platform. The software is particularly suitable for ChIP-Chip and ChIP-Seq analysis, and has also been used with RNA-Seq and as a stand-alone motif management system.
The MochiView website (link) contains everything you need to get started, including a tutorial and a few sample videos of the software in use (link).
Here is a summary of some of MochiView's features:
 Highly customizable plots… display anything from genome alignments to motif matches to bar- or line-graph data on one or more tracks. Open plots are persistent across sessions and you can save your configurations for later use
 The plots have smooth scrolling/zooming, lots of interactive elements, and a powerful data browser feature.
 Very easy to set up and use. The database is built in to the software, so no fussing around with external databases is required. You can also export your current database and plot configurations to share with other MochiView users.
 Motif management and analysis utilities:
- MANAGEMENT: Maintain a motif database (several libraries are available on the website to get you started)
- DISCOVERY: Find new motifs with the built in motif finder (or import MEME and Bioprospector motif searches)
- COMPARISON: Check whether your newly found motifs resemble any other known motifs
- DISTRIBUTION: Search for non-random positioning of motif matches relative to other genomic features such as start codons or instances of a different motif.
- MOTIF ANALYSIS and ROC PLOT: Determine whether your ChIP regions are enriched for a motif relative to a set of control regions
- MOTIF SCORING: Numerous options for motif scoring (LOD score, p-values, w-score) and many different export formats. For example, a few clicks gives you a "gene vs motif" spreadsheet matrix of the motif score for each gene's promoter region.
- MOTIF LOGOS: Export logos of one or more of the motifs in your library
- MOTIF GO TERM ENRICHMENT: Determine whether your motif is enriched in the promoters of genes with common functionality
 Location and data analysis and refinement utilities:
- PEAK EXTRACTION: Not a full-fledged peak finder (i.e. no p-values), but this utility does an excellent job of smoothing your ChIP-Chip data and marking regions of a user-defined width under peaks (a useful first step to refining a motif search).
- DATA SMOOTHING: Smooth your data and save as a "Tiled Set" (similar to a UCSC browser wig track).
- DATA REFINEMENT: Numerous filters can refine your data sets (e.g. filter by value or by overlap with other sets of locations).
- LOCATION SET SUMMARY/COMPARISON: Get a detailed description of the genome-wide coverage of one or two set of locations (e.g. ChIP binding regions)
- GENE PROXIMITY ASSIGNMENT: Determine which gene(s) lie near a set of locations (e.g. ChIP binding regions). Can be used in conjunction with a GO term enrichment analysis.
- SET OPERATIONS: Take the intersection, union, or difference of two sets of locations (e.g. find the overlap of two sets of binding regions and remove the portions that overlap ORFs)
 Extensive sequence search options, including direct and inverse repeats
Thanks for your time!
Edited by mochiview, 20 November 2009 - 02:55 PM.