Internet Contig Explorer (iCE)--A Tool for Visualizing Clone Fingerprint Maps

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
Genome Research (Impact Factor: 14.63). 07/2003; 13(6A):1244-9. DOI: 10.1101/gr.819303
Source: PubMed


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.

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    • "To identify overlapping BAC clones, high-resolution agarose gel fingerprinting of DNA digested with EcoRI/EcoRV (Marra et al. 1997) was performed by the Genome Sciences Center, British Columbia Cancer Agency, Canada. Contigs were assembled with FPC with a tolerance of 7 and cutoff of 1e -12 and visualized using Internet Contig Explorer v3.5 (Fjell et al. 2003). "
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    ABSTRACT: Major Histocompatibility Complex (MHC) genes are a central component of the vertebrate immune system and usually exist in a single genomic region. However, considerable differences in MHC organization and size exist between different vertebrate lineages. Reptiles occupy a key evolutionary position for understanding how variation in MHC structure evolved in vertebrates, but information on the structure of the MHC region in reptiles is limited. In this study, we investigate the organization and cytogenetic location of MHC genes in the tuatara (Sphenodon punctatus), the sole extant representative of the early-diverging reptilian order Rhynchocephalia. Sequencing and mapping of 12 clones containing class I and II MHC genes from a Bacterial Artificial Chromosome library indicated that the core MHC region is located on chromosome 13q. However, duplication and translocation of MHC genes outside of the core region was evident, as additional class I MHC genes were located on chromosome 4p. We found a total of seven class I sequences, and eleven class II β sequences, with evidence for duplication and pseudogenization of genes within the tuatara lineage. The tuatara MHC is characterized by high repeat content and low gene density compared with other species and we found no antigen processing or MHC framework genes on the MHC gene-containing clones. Our findings indicate substantial differences in MHC organization in tuatara compared with mammalian and avian MHCs and highlight the dynamic nature of the MHC. Further sequencing and annotation of tuatara and other reptile MHCs will determine if the tuatara MHC is representative of non-avian reptiles in general. Copyright © 2015 Author et al.
    Full-text · Article · May 2015 · G3-Genes Genomes Genetics
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    • "All V H þ , C H þ and V H þ C H þ clones were restriction fingerprinted using Internet Contig Explorer (iCE) (Fjell et al., 2003 "
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    ABSTRACT: We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations. J. Exp. Zool. (Mol. Dev. Evol.) 9999B: 1-26, 2014. © 2014 Wiley Periodicals, Inc.
    Full-text · Article · Sep 2014 · Journal of Experimental Zoology Part B Molecular and Developmental Evolution
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    • "Filters were visualized using BioMax film (Kodak). BAC clones were chosen based on the physical BAC fingerprint map for Atlantic salmon [70] that is publicly available on the internet Contig Explorer (iCE) version 3.5 [71]. The BAC end sequence information, that is available in ASalBase [72], was also used for selection of the BAC clones. "
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