CGView

CGView generates detailed graphical maps of circular genomes to visualize sequence features, base composition, and comparative BLAST results for genomic analysis.

Key Features:

• Supported input formats: Accepts raw sequence, FASTA, GenBank, or EMBL files and optional GFF files for additional feature or analysis annotations.
• Graphical mapping: Produces circular genome maps that display sequence features, base composition plots, and layered analysis results with both whole-genome overviews and detailed regional views.
• Sequence comparison (BLAST): Performs BLAST comparisons of a primary sequence against up to three genomes or sequence sets.
• Comparative analysis outputs: Highlights conserved genomic segments, candidate horizontal gene transfer events, and variations in gene copy number.
• Integration of new sequence data: Allows newly obtained sequence reads to be used as comparison inputs to map onto reference genomes and assess genome coverage.
• Visualization customization: Enables selection of which feature types are displayed and how features are visually represented on maps.

Scientific Applications:

• Circular genome visualization: Visualization of bacterial, plasmid, chloroplast, and mitochondrial genome structure and annotated features.
• Comparative genomics: Visualization of sequence conservation and genomic differences across species or strains using BLAST-based comparisons.
• Horizontal gene transfer detection: Identification and visualization of putative horizontal gene transfer regions through comparative mapping.
• Gene copy number assessment: Detection and visualization of gene copy number variation across compared genomes.
• Read mapping and coverage assessment: Mapping of user-provided sequence reads onto reference genomes to evaluate coverage and novel sequence integration.

Methodology:

Parses input sequences in raw/FASTA/GenBank/EMBL formats with optional GFF annotations, performs BLAST comparisons against up to three genomes or sequence sets, and generates circular maps with feature layers and base composition plots; user-supplied reads may be used as comparison input to assess mapping coverage.