Internet Contig Explorer version 3
Third release of internet map viewer
Vancouver, BC, Canada | The Genome Sequence Centre has been developing an online tool to view physical map data. The Internet Contig Explorer is a Java based tool that allows users to navigate through physical maps of various organisms and provides views and information on contigs, clones and markers.
iCE complements the functionality of FPC, by providing scientists with a read-only cross-platform dynamic viewer. The focus of iCE is to present the data in an intuitive and available manner, making it straightforward to poll the physical map for specific information about clones, markers and contigs. Users can search for and display individual clones, contigs, clone fingerprints, clone insert sizes and markers and can load into the software user-generated lists of clones and view their fingerprints. iCE is being used at our Genome Centre to offer up to the research community views of the mouse, rat, bovine, C. briggsae and several fungal genome BAC fingerprint maps we have generated or are constructing.
Fingerprint maps have proven useful in various applications, supporting both whole-genome and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have been generated for several genomes, including those of Caenorhabditis elegans, human, mouse, Arabidopsis thaliana, rice and the nematode Caenorhabditis briggsae. Fingerprint maps of other genomes, including those of fungi, bacteria, the laboratory rat and the cow, are being generated. The increased interest in fingerprint maps has spawned a need in the research community for intuitive computer tools that facilitate viewing of the maps and the underlying fingerprint data.
With an internet connection, iCE provides a way to download and locally cache current map data. With the newly implemented cache feature is best suited for slower intenet connections, in cases where downloading the latest data would be too time consuming, or for portability, where internet availability cannot be assured.
Anyone with an internet connection and Java-complient operating system can view and manipulate physical maps and associated data.
Original gel images, marker data and clone information is incorporated into the map view. Detailed clone information, such as the number and sizes of bands, is available and can be exported to a flat-text file for postprocessing.
While browsing the map, detailed clone and marker information is available.
iCE can be used as a tool to extract specific information about clones and markers. Below are shown the report screens which provide a means to export map data to text files.