GenBank and FASTA Plasmid Map Viewer with Annotations
Explore the versioned pUC19 cloning-vector sequence as a circular map, feature list and nucleotide sequence. The workspace connects restriction sites and annotations to explicit coordinates. This reference is a cloning vector, not an invented affinity-tagged expression construct, and it distinguishes record annotations from features inferred by sequence matching.
The shipped 2,686 bp circular pUC19 example pins its GenBank accession, sequence hash, feature library, enzyme table and primer data versions. Its source title is retained. No promoter, affinity tag or open reading frame is added solely to fit a marketing description.
Read a plasmid map as a view of a specific sequence
The map is useful because it places features and restriction sites on a shared coordinate system. It is not an independent experimental observation. Every graphical element should trace back to a sequence position or a declared annotation. Start by confirming molecule length, circular topology and the accession version before comparing a familiar-looking map with a laboratory stock.
The pUC19 reference is pinned to a retained record rather than fetched from an unversioned name on every visit. This makes it possible to reproduce the same sequence-based calculations. An actual laboratory derivative may contain mutations or inserted material, so its name alone is insufficient evidence that it is identical to the reference. Import the actual sequence where it is available.
Distinguish annotation provenance from appearance
A feature can originate in a submitted record or be inferred by matching a library sequence. These routes of evidence are different even when the resulting arrow has the same colour and label. Inspect strand, interval and supporting source, especially for partial or overlapping matches. A visually complete coding feature can still require examination of its translation and boundaries.
Before exporting a map for a protocol or presentation, retain the sequence identifier, data versions and any edits. If you add an insert or change the origin, the resulting construct should receive a distinct identity. The map can support planning, restriction analysis and communication, while sequence confirmation remains necessary to establish the actual material present in a clone.
Equations and variables
Inclusive sequence interval
L = end − start + 1
- L
- Length of a non-wrapping interval (nt)
- start, end
- One-based inclusive coordinates on the stated reference sequence
Circular coordinate normalisation
pwrapped = ((p − 1) mod L) + 1
- p
- One-based coordinate before wrapping
- L
- Circular sequence length (bp)
- pwrapped
- Equivalent coordinate on the stated circular sequence
Scope and limitations
- FASTA provides sequence and a header, not a complete feature table. Feature matches inferred from a library are distinct from annotations supplied by a GenBank record.
- A sequence match establishes similarity under the matching rule, not biological activity of a promoter, origin or coding sequence in a chosen host.
- Circular origin and strand orientation affect coordinates. Preserve topology and accession version with exports and comparisons.
Sources and provenance
- GenBank pUC19 record L09137.2Existing source notice: NCBI public domain
Versioned sequence and SHA-256 are pinned in the shipped example.
- NCBI GenBank feature-table definitionsNCBI source terms; documentation reference
Technical questions
Why can a FASTA file show fewer annotations than GenBank?
FASTA generally contains residues and a descriptive header. GenBank can carry a structured feature table with locations and qualifiers. Any features inferred after FASTA import should retain their inference label rather than being presented as annotations submitted with the original record.
Can the map prove that a promoter works?
No. A matching sequence can identify a candidate feature or reproduce a record annotation. Promoter function depends on host, orientation, neighbouring sequence and experimental conditions. Functional interpretation requires evidence beyond a circular drawing or sequence match.
Why do coordinates change when the circular origin moves?
A circular molecule has no unique first base, but a file chooses one to number positions. Rotating that origin changes displayed coordinates while preserving the circular sequence. Keep the origin convention or a sequence hash when comparing maps from different files.
Connected workflows
- Virtual restriction digest and fragment sizes
Calculate restriction fragments from the same sequence.
- Six-frame translation and ORF inspection
Inspect coding potential and translation conventions.
- Vector and insert molar-ratio calculation
Use the vector identity in DNA-amount planning.