E2G

E2G maps expressed sequence tags (ESTs) and complementary DNA (cDNA) sequences to user-supplied genomic DNA for large-scale transcript-to-genome alignment and analysis.

Key Features:

• Precomputed indexed data structures: Uses precomputed indexed formats to optimize sequence comparison and accelerate mapping of ESTs and cDNAs to genomic DNA.
• Large EST repository: Hosts extensive EST collections, e.g., 4.1 million mouse ESTs amounting to 1.87 gigabases (Gb), in indexed form for rapid comparison against user-supplied genomic sequences.
• High-throughput mapping: Supports mapping of large datasets of EST and cDNA sequences to genomic DNA, enabling scalable analysis of transcript-to-genome alignments.
• Exportable mapped sequences: Produces mapped EST/cDNA sequences as outputs that can be downloaded for downstream analyses.

Scientific Applications:

• Gene annotation: Aligning ESTs and cDNAs to genomic DNA to inform exon–intron structures and annotate gene models.
• Novel transcript identification: Detecting previously unannotated transcripts and transcript variants by mapping EST and cDNA evidence to the genome.
• Comparative genomics: Comparing mapped transcript data across genomes to study conservation and divergence of expressed sequences.

Methodology:

Utilizes precomputed indexed data structures to optimize sequence comparison and map EST and cDNA sequences onto user-supplied genomic DNA.