Vectors
Plasmid map and GenBank
Read a GenBank file and draw a circular or linear plasmid map, with GenBank, FASTA, SVG and PNG output. No file is ever uploaded.
Features
This file carries no features. A raw sequence or FASTA gives an empty map; supply a GenBank file to see promoters, tags and resistance markers.
Everything is processed in your browser and no file is uploaded. The GenBank output opens again in SnapGene, Benchling and ApE. Feature labels are taken from label, gene, product or note, in that order of preference.
Formula
LOCUS → FEATURES → ORIGIN
- LOCUS
- the first line: name, length in base pairs, and circular or linear
- FEATURES
- the feature list; each has a type, a location and a set of qualifiers
- ORIGIN
- the sequence itself, in blocks of ten with sixty bases per line
- complement()
- the feature sits on the opposite strand
- join()
- the feature is built from separate pieces — exons, or a span across the origin
Worked example
Working out which strand a feature is on, and where
- CDS complement(1400..2260)
- /label="AmpR"
- The two numbers are coordinates on the top strand, counted from one.
- The word complement means the gene sits on the bottom strand and reads from 2260 towards 1400.
- Its length is 2260 minus 1400 plus one.
- On the map its arrow points anticlockwise.
Answer the ampicillin resistance gene, 861 bp, on the reverse strand
Common mistakes
- Copying only part of a GenBank file. If the ORIGIN block or the closing double slash is missing, the sequence is not read and the map comes out empty.
- Expecting a FASTA file to carry features. FASTA is sequence only; for promoters, tags and resistance markers either supply a GenBank file or run the auto-annotator.
- Forgetting that GenBank coordinates start at one, not zero. If you are working with output from a program that counts from zero, everything will be off by one.
- Leaving a plasmid marked as linear. Features spanning the junction between the end and the start, and restriction sites in that region, will then be missed.
Frequently asked
Where does the feature label come from?
From the label, gene, product, note and standard_name qualifiers, in that order of preference. If none is present the feature type itself is shown. SnapGene and Benchling use the same order.
Will the GenBank output open in other software?
Yes. Standard format is written and a full round trip is tested: length, sequence, feature count, strand and join locations all survive.
Why are some features drawn on outer rings?
Two overlapping features cannot share a ring. Each feature goes on the innermost ring where it does not collide, so the distance from the centre carries no biological meaning.