gbatlas

gbatlas renders interactive linear and circular feature maps for GenBank and GenPept records, enabling local browser-based visualization of annotated sequences with computed analytical layers.

Key Features:

• File format support: Opens .gb, .gbk, .gbff, .gp and plain GenBank text files, including multi-record files.
• Interactive feature maps: Renders linear and circular feature maps, including circular plasmid maps, alongside annotated source text and nucleotide/protein sequence.
• CDS translation validation: Translates CDS features using the record's own genetic code and translation qualifiers, and flags discrepancies between stored /translation and plain translation.
• Computed analytical layers: Adds optional ORF prediction and restriction-site mapping layers.
• Sequence selection and export: Allows dragging a range in the sequence band to select it, then copying either strand as DNA or protein in plain or FASTA format.
• Feature filtering: Filters features by type.
• Local session persistence: Keeps open records as local sessions for recovery after closing a tab.
• Local-only processing: Runs entirely in the browser with files never uploaded to a server.

Scientific Applications:

• GenBank record visualization: Interactive exploration of annotated GenBank and GenPept records with dual map representations.
• Plasmid map generation: Circular plasmid map rendering for vector and construct analysis.
• CDS annotation verification: Validation of stored translations against computed translations using genetic code and translation qualifiers.
• ORF analysis: Prediction and visualization of open reading frames across sequences.
• Restriction mapping: Computational mapping of restriction enzyme sites.
• Sequence extraction: Targeted retrieval of specific regions in DNA or protein format for downstream use.

Methodology:

gbatlas detects file format from file content rather than extension, parses GenBank and GenPept records, translates CDS features using the record's specified genetic code and translation qualifiers, and computes ORF prediction and restriction-site mapping as optional layers.