WebGMAP

WebGMAP aligns cDNA and EST sequences to genomic DNA to support genome annotation, gene structure determination, and analysis of alternative splicing and polyadenylation.

Key Features:

• cDNA–Genome Alignment: Integrates GMAP for mapping cDNAs and ESTs onto genomic sequences to identify exon–intron structures and splice sites.
• Sequence analysis functions: Provides nucleotide positioning, six-frame translations, sequence reverse complementation, and imperfect motif detection and alignment.
• Data processing: Supports sorting, filtering, and searching of cDNA and alignment datasets for focused analysis of sequence sets.
• EST-Genome-Browser: Displays annotated gene structures and cDNA–genome alignments at scales from 100 to 50,000 nucleotides and highlights base differences between query cDNAs and the genome.
• Variant indication: Identifies and highlights potential point mutations and insertion–deletion variations between cDNAs/ESTs and the reference genome.

Scientific Applications:

• Genome annotation: Refinement of gene models and exon–intron boundaries through integrated cDNA/EST alignment evidence.
• Gene structure analysis: Determination of alternative splicing patterns and isoform structures from cDNA and EST alignments.
• Polyadenylation studies: Analysis of polyadenylation patterns using aligned cDNA/EST sequences.
• Variation detection: Detection and characterization of point mutations and indels relative to the genomic reference.

Methodology:

Performs cDNA–genome alignment using GMAP, maps cDNAs/ESTs to genomic sequences, computes six-frame translations and reverse complements, detects and aligns imperfect motifs, displays annotated gene structures and alignments at 100–50,000 nucleotide scales, and highlights base differences between query cDNAs and the genome.