Category Cross-Omics>Sequence Analysis/Tools, Genomics>Genetic Data Analysis/Tools, Cross-Omics>Next Generation Sequence Analysis/Tools, Genomics>Gene Expression Analysis/Profiling/Tools

Abstract GenPlay is a multi-purpose genome analyzer and browser that can be used for rapid analysis and data processing. It is written in Java and runs on all major operating systems.

GenPlay recognizes a wide variety of common genomic data formats from microarray or sequencing based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualisable tracks.

GenPlay displays tracks adapted to summarize gene structure, gene expression, repeat families, CPG islands, etc. as well as custom tracks to show the results of RNA-Seq, ChIP-Seq, TimEX-Seq and SNP analysis. GenPlay can generate statistics (minimum, maximum, standard deviation, correlation, etc).

The tools provided include Gaussian filter, peak finders, signal saturation, island finders.

The software also offers graphical features such as scatter plots and bar charts to depict signal repartition. The library of operations is continuously growing based on the emerging needs.

GenPlay was developed with the aim of producing a graphically oriented, user friendly multi-purpose tool that would help biologists visualize, analyze and transform their raw data into biologically relevant tracks.

It was also developed to facilitate comparison of datasets generated on multiple platforms.

GenPlay Website features -- GenPlay can be launched from a dedicated website at the manufacturer’s website (Main_Page).

The user starts GenPlay using a Web Start procedure that also allocates a specific amount of memory to the software. The number of tracks and the level of resolution of the tracks that can be loaded concurrently are limited by the amount of memory selected at start up.

A Library link accessible from the Main page of the website contains annotation and configuration files for the last versions of the human and mouse genome assemblies.

Configuration files must be downloaded and installed to work with an assembly and a genome different from the default, which is human hg19. Commonly used annotation files can also be found in the Library or can be accessed through the integrated DAS client.

Help files are available through the Documentation link. Detailed information on all operations and on all formats recognized by GenPlay is available. The manufacturers strongly recommend that users read the documentation before starting to work with GenPlay.

There is also a tutorial page, showing an example of ChIP-Seq analysis and an example of TimEX analysis. There are detailed examples of how to use the operations of the software.

A link allows users to report bugs, ask for new functionalities and submit ideas for future development.

The FAQ page compiles the frequent questions received from users followed by the manufacturer’s answers. Older versions of GenPlay are also available for download from the website. Being open source, the source code is available from the link specified on the About page.

GenPlay Graphical User Interface (GUI) -- The interface that the manufacturers designed is similar to a music recording or commonly used spreadsheet software and consists of a list of tracks composed of rows that contain independent datasets.

Each row can be expanded, collapsed or moved the same way rows move in a spreadsheet. Chromosomal location can be changed by simply dragging the mouse while the wheel allows the user to zoom in and out, seamlessly from a 1 base resolution to a whole chromosome view.

On top of the track list there is a ruler that shows the position of the displayed window on the selected chromosome or scaffold. All operations available for loaded tracks are initiated by a right mouse click on the track handlers which reveals dynamic menus.

The Control Panel, located right under the track list, allows navigation in the genome. The zoom, the position and the chromosome or scaffold selection can be modified from there as well.

In addition, genomic position can be specified in a text field. The last part of the interface is the status bar at the bottom of the window that allows the user to monitor memory usage.

The status bar displays text messages describing the current operation, as well as the time elapsed since the beginning of the operation and the percentage complete. The stop button offers the opportunity to cancel most operations while they are in progress.

On the top left of the software interface there is an option button that controls the general configuration, toggles the full screen mode and saves the current project (all the tracks from the list except the sequence tracks).

GenPlay Track Types -- The track types currently available in GenPlay are the Variable Window tracks, Fixed Window tracks, Gene tracks, Sequence tracks, SNP tracks, and Repeat tracks.

Variable Window tracks allow the visualization of the position and of the score of interval of variable sizes. These tracks are adapted to the visualization of data that can be summarized on genomic intervals of predefined size. The prototypic datasets are microarray experiments in which each interval represents a probe or a gene.

Fixed window tracks are most useful to visualize raw sequencing results that have Not been projected to annotations. This track type is particularly adapted to the visualization of ChIP-Seq, RNA-Seq and Timex-Seq experiments.

To create a Fixed Window track, the software divides the genome into bins of fixed size and then computes how many reads fall into each bin. The bin size is selected by the user. Users also define the method of computation of the scores of each bin (sum, max, or average number of the scores per bin).

Both Fixed and Variable Window tracks can only display a single value per interval. When data containing overlapping intervals are loaded, GenPlay summarizes the interval according to user selected parameters.

In the case of Variable Window tracks, GenPlay calculates the intersection between all overlapping intervals, creating new intervals whenever necessary.

The score of each new interval can be the weighted average, the maximum, or the weighted sum of each overlapping interval score. In the case of Fixed Window tracks, GenPlay computes the weighted intersection of all overlapping intervals with the fixed sized bins and assigns the scores.

In the case of sequencing data, the problem of overlapping intervals can be avoided by only considering the start position of each read. This latter solution is the default mode in GenPlay for loading files that are the output of sequence aligners (such as, Bowtie, Eland, etc.).

Gene expression results often must be visualized in tracks where a single genomic interval can have multiple values, for instance to visualize the expression of multiple isoforms or overlapping genes.

To allow this type of analysis, the manufacturers have developed Gene tracks. Gene tracks can be used to visualize data containing overlapping intervals without summarizing the intervals.

Gene Tracks also allow the visualization of exon and intron boundaries and of a score, which can be associated either to the whole gene or to each exon.

Scores are visualized by color coding the exons; numeric scores are displayed when the mouse cursor hovers on a gene or on a gene exon. Genes (or other objects) visualized on a Gene Track can be hyperlinked to various databases allowing the software to open a page in a browser showing details about a selected gene.

Sequence tracks display the nucleotide sequence of the selected genome assembly. This is the only track where the data is Not completely loaded in memory. The software reads a file in random access memory only when there is enough room on the screen to print all the nucleotides.

SNP tracks display the frequency at which each base has been found in a particular sample.

Repeat tracks display repeat windows organized by family or class.

GenPlay Operations -- Each track type has different operations available -

In the case of Fixed Windows tracks, GenPlay offers normalization, standard score, indexation, Gaussian smoothing, moving window average, Loess regression, correlation calculation, various filters, peak finding, as well as many arithmetic, statistical and masking operations, etc.

Note: The different track operations available for each track type are fully documented on the Documentation page of the manufacturer's website.

GenPlay Memory requirements -- High memory usage is the major trade-off that the manufacturers had to make in order to obtain higher performance.

GenPlay can be started with very little memory whereas most genome-wide analysis for mammalian datasets requires a minimum of 4 GB and preferably 8 GB of RAM.

Working on multiple tracks at the base pair level can be done in GenPlay if a workstation is available. The manufacturers routinely perform such analysis using an 8 processor work-station with 24 GB of RAM.

System Requirements

Contact manufacturer.


Manufacturer Web Site GenPlay

Price Contact manufacturer.

G6G Abstract Number 20793

G6G Manufacturer Number 104321