Know what your file contains.

File handling

The browser imports GenBank and FASTA through TeselaGen bio-parsers. SnapGene .dna and AB1 use local readers checked against Biopython on a public test-file corpus. The checks cover sequence letters, feature segments, primer coordinates, chromatogram channels and quality scores. They do not establish compatibility with every file produced by every software or instrument version. The editable representation contains a sequence and its supported annotations. Original file bytes are retained separately in the project, so information the parser does not represent remains recoverable. Parser messages are displayed in the file status line; hover over a shortened status to read the complete message.

A .pmap project is versioned JSON containing the current sequences, annotations and imported originals. It can be downloaded and reopened on another computer. It is not encrypted. Native .dna export with edited data is not implemented; choosing Original file downloads the unchanged source. GenBank is a conversion, and FASTA contains no feature annotations. Keep the source when format-specific history, metadata or display settings matter.

Editing and coordinates

The workspace uses Open Vector Editor, with circular, linear and base-level views. Its internal annotation coordinates are zero-based and inclusive; user-facing sequence positions are one-based. Features can span the origin of a circular sequence. Editing operations update supported annotation positions through the editor's sequence model. Check affected features after a sequence edit, especially when converting a file with compound or unusual annotations.

Undo and redo are editing-session operations. A saved project stores the current state and original imports; it does not store the complete undo stack. The browser recovery copy is local to this domain and browser profile. Export a project before clearing site storage or changing devices.

Restriction sites, digestion and PCR

Restriction recognition data comes from the MIT-licensed TeselaGen sequence-utils distribution. Recognition sites are sequence matches. The digest view represents predicted fragments from selected cuts, not measured gel migration or reaction completion. Fragment lengths are checked against 72 Biopython cases covering linear and circular sequences and 12 enzymes. Coincident cuts are combined, and an uncut molecule retains its full length. Partial-digest mode lists possible contiguous fragments, not their relative abundance. Enzyme activity, methylation, star activity and buffer conditions require a separate experimental check. This release does not claim a vendor-maintained enzyme database.

The PCR view uses the locations of annotated forward and reverse primers to construct a sequence product, including explicitly supplied primer bases. It is not a specificity search against a genome and does not establish whether a primer pair will amplify experimentally. The melting-temperature display uses SantaLucia nearest-neighbor parameters with 50 nM total DNA, 50 mM sodium, 1.5 mM magnesium and 0.6 mM dNTP. It includes the self-complementarity correction and is checked against 225 Biopython calculations. It requires 2–200 unambiguous DNA bases; otherwise the display says unavailable. These fixed conditions are not an assay-specific temperature recommendation. ORF display identifies sequence patterns and does not establish expression.

Scope and sources

AB1 import displays the called sequence and available chromatogram data. Automatic chromatogram trimming, reference alignment, full cloning workflows and lossless edited SnapGene round trips are not yet part of this release. The default upstream alignment-server command is removed. No sequence analysis request is sent to that service.

The example pUC19 sequence is NCBI accession M77789.2, retrieved September 26, 2026. Genetic-code references are available separately at Codon Chart. Open Vector Editor 0.8.42 and bio-parsers 0.4.38 are pinned; third-party notices accompany the application.

Portable projects are limited to 32 MB. New project downloads a copy of the current project before clearing the workspace.