iCE - internet Contig Explorer

iCE - internet Contig Explorer provides visualization and analysis of fingerprint clone physical maps, including clone fingerprints, contigs, insert sizes, and markers, to support contig assembly, BAC clone selection, sequencing, and gene-cloning projects.

Key Features:

• Fingerprint data display and analysis: Displays and analyzes fingerprint clone physical maps, clone fingerprints, contigs, insert sizes, and genetic markers and supports queries for individual clones.
• Custom data loading: Imports lists of specific clones to focus analysis on selected genomic regions and displays the corresponding fingerprint data.
• Multi-species support: Supports genomes including mouse, rat, cow, Cryptococcus species, and multiple fungal and bacterial BAC maps.
• Integration with sequencing projects: Integrated into sequencing workflows and used in the Rat Genome Sequencing Project to manage and provide rat BAC clones for sequencing at the Human Genome Sequencing Center, Baylor College of Medicine.

Scientific Applications:

• Whole-genome and region-specific sequencing: Facilitates contig-based whole-genome and targeted region sequencing by providing detailed clone and contig fingerprint information.
• Gene cloning studies: Supports identification and isolation of genes by mapping clone fingerprints and markers to genomic regions.
• Comparative genomics: Enables cross-species comparative analyses using supported genomes and BAC maps to study evolutionary relationships and functional genomics.

Methodology:

Implemented in Java; imports lists of clones and displays corresponding fingerprint map data.