Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.

TitleInternet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.
Publication TypeJournal Article
Year of Publication2003
AuthorsFjell, CD, Bosdet, I, Schein, JE, Jones, SJM, Marra, MA
JournalGenome Res
Volume13
Issue6A
Pagination1244-9
Date Published2003 Jun
ISSN1088-9051
KeywordsAnimals, Arabidopsis, Caenorhabditis, Caenorhabditis elegans, Cloning, Molecular, Contig Mapping, DNA Fingerprinting, DNA, Helminth, DNA, Plant, Humans, Internet, Mice, Oryza, Rats, Software
Abstract

Fingerprinted clone physical 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 human, mouse, rat, the nematodes Caenorhabditis elegans and Caenorhabditis briggsae, Arabidopsis thaliana and rice. Fingerprint maps of other genomes, including those of fungi, bacteria, poplar, and the cow, are being generated. The increasing use of fingerprint maps in genomic research has spawned a need in the research community for intuitive computer tools that facilitate viewing of the maps and the underlying fingerprint data. In this report we describe a new Java-based application called iCE (Internet Contig Explorer) that has been designed to provide views of fingerprint maps and associated data. Users can search for and display individual clones, contigs, clone fingerprints, clone insert sizes and markers. Users can also load into the software lists of particular clones of interest 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 bacterial artificial chromosome (BAC) fingerprint maps we have either completed or are currently constructing. We are also using iCE as part of the Rat Genome Sequencing Project to manage our provision of rat BAC clones for sequencing at the Human Genome Sequencing Center at the Baylor College of Medicine.

DOI10.1101/gr.819303
Alternate JournalGenome Res.
PubMed ID12799356
PubMed Central IDPMC403654