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.

Text imports are checked before parsing: unsupported sequence letters, empty FASTA records and malformed GenBank ORIGIN text reject the whole file. The normalized sequence of every record is checked again against the reader's output, so a reader cannot silently shorten the DNA by discarding characters. GenBank records need local ORIGIN sequence data; remote CONTIG references are not fetched.

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.

Annotation map and feature DNA

The overview is drawn directly from the current sequence and its annotations. The library lists every supported feature and primer. Source features are hidden by default; select the source type or include Source to see them. Search and type filters determine which annotations appear in the map and its SVG or PNG export. The map draws up to 80 matches and labels up to 20, plus the selected annotation. For dense maps, narrow the filter; the list remains the exact coordinate reference. Colors distinguish annotations and do not indicate biological function.

Select a feature to inspect one-based inclusive positions, strand, segment length and GC percentage. GC uses only A, C, G and T in its denominator. Feature DNA joins its stored segments, excludes intervening gaps and is reverse-complemented for a reverse annotation. Coordinates are those in the imported or edited sequence model; this does not infer a mature transcript, coding frame, primer tail or uncertain boundary. Select in editor selects the whole annotation span, which may include gaps. Feature extraction is checked against 34 Biopython 1.85 cases, including split and origin-crossing annotations.

SVG preserves editable vector shapes and labels. PNG is up to 2,400 pixels wide; very tall linear maps are scaled proportionally to an 8,000-pixel height limit. The map layout does not change the sequence or its topology. A circular sequence displayed linearly is opened at base 1.

Detected features

The workspace compares each sequence with a library of 13 feature sequences copied exactly from annotated NCBI GenBank records. It searches both strands and, on a circular sequence, across the origin. A hit is drawn with a dashed outline and labelled detected by exact sequence match. It is not an identification or verification of a construct. One differing base prevents a match, a variant needs its own library entry, and a match does not show that the element is complete or functional in your sequence. Detected features stay out of your annotations, exports and project until you choose Add to annotations. An added feature carries a note naming its source record and location. Detection is checked against a separate Python scan of seven sequences, including pUC19 rotated so a hit spans the origin, its reverse complement, and a single-base variant that must not match.

AmpR and NeoR/KanR each have two entries, from records whose copies differ at two bases. lacZα is left out because it contains each vector's own polylinker, so an exact copy from one record would not match another vector. The f1 origin and the T7 and lac promoters are left out because none of these records annotates them as a region.

Sequence search and zoom

Find a DNA sequence searches a 2–1,000-base IUPAC pattern on the forward strand, reverse strand or both. Circular sequences also include matches crossing the origin, without traversing the molecule more than once. Positions are one-based, inclusive and measured on the original forward sequence; strand labels identify the orientation. A query identical to its reverse complement appears once as Both strands. For that case, the DNA preview shows the forward strand.

By default, every interpretation of an ambiguous sequence base must satisfy the query to count as a definite pattern match. Include possible matches also shows positions where some interpretations fit, marked Possible. For example, a query ATG only possibly matches ANN; a query ANN definitely matches ATG. This does not resolve uncertain base calls. Search allows no mismatches or gaps and is not a primer-binding or specificity prediction. The 500-result limit is explicit; refine a query when more matches exist. Search is checked against 118 Biopython and exhaustive ambiguity cases.

Selecting a match highlights it on the map and offers DNA or coordinate-TSV downloads. Original sequence coordinates remain ascending along the forward strand even when the exported DNA is reverse-complemented. A start larger than the end crosses a circular origin. Editing the sequence or changing the query clears old matches. The highlight is a view overlay, not an annotation added to the project. SVG/PNG includes the current highlight. Zoom changes the viewport only; exports retain the complete map.

Restriction sites, digestion and PCR

The public primer Tm calculator exposes the same DNA_NN3 parameters with editable concentration settings, a Primer3-equivalent default, a PCR primer-in-excess model for one or two primers and sourced annealing starting points. The molarity, single-step dilution and ligation pages state their formulas and units separately. They do not alter the sequence editor's fixed Tm settings or infer experimental outcomes.

The molar mass calculator and molarity's formula option use a pinned CIAAW 2024 abridged atomic-weight table. Integer atom counts, balanced groups and middle-dot hydrates are supported; isotope-specific masses, charges and chemical-identity inference are not. Eighty independently counted formula cases check parsing and mass summation. The serial dilution planner uses a constant factor and mixed volume, explicitly accounts for onward transfers and optional last-tube discard, and is checked against 48 exact-rational solute/volume ledgers. It does not model pipetting uncertainty.

The qPCR standard-curve worksheet fits Cq versus log10(quantity), weighting every entered well equally and retaining replicates. The efficiency formula follows Bio-Rad's iCycler iQ manual; the page links the source and explains the base-10 convention. Forty-one independent NumPy fits check slope, intercept, R², efficiency, fitted Cq and residuals. A fit does not establish specificity, detection limits or assay validity.

The editor opens its cut-site view on a Common commercial group of 56 enzymes and shows those that cut once. Their recognition sites and cut offsets come from the REBASE-derived restriction data in Biopython 1.85, which lists each of them as supplied by New England Biolabs. The map's cut-site ticks and its Unique cutters list use the same table. Each number is the one-based base after which the top strand is cut. Cut positions are checked against Biopython 1.85 on 18 sequences, including pUC19, pBR322, linear and circular molecules, both strands and sites spanning the origin. The editor's full enzyme list, from the MIT-licensed TeselaGen sequence-utils distribution, stays available in its cut-site menu and digest view. 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. Supplier data is a dated snapshot rather than a live catalogue, and 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.

Overlap assembly

Assemble fragments joins two to eight prepared linear DNA records in the order and orientation you choose. Inputs must contain only A, C, G and T. A circular source is refused: supply its intended linear fragment first. Selecting a circular product does not choose a restriction cut, simulate PCR or make the input plasmid linear.

The suffix of one fragment must exactly match the next fragment's prefix. Search defaults to 15–80 bases and can be set within 10–200 bases; these are search bounds, not recommended experimental conditions. Every matching length is shown. If several lengths fit, you must choose one. A circular product also requires an exact last-to-first overlap. Each overlap appears once in the result, whose base 1 is the first base of the oriented first fragment. Each fragment must have bases between its incoming and outgoing overlaps; fully redundant or intersecting overlap regions are refused.

The tool also lists other matching ends among the selected fragment orientations, including self-joins. This is not exhaustive product enumeration: internal repeats, other orientations, mismatches and reaction chemistry are outside the model. Gibson assembly uses overlapping ends, but overlap length and experimental suitability depend on the design and conditions; see NEB's assembly guidance. A matching construct is not a yield or biological-function prediction.

Source feature coordinates, compound segments and strand follow the oriented DNA, including a circular product's origin. Original feature qualifiers remain source information; they are not revalidated after assembly. Overlapping or out-of-order feature segments are refused. Input source annotations and primer annotations are omitted and counted in the report. Components and overlap regions receive separate annotations. Overlapping annotations from different input fragments remain separate rather than being merged by name.

The result is limited to 250,000 bases and 5,000 annotations; combined inputs are limited to 252,000 bases. Download GenBank or FASTA directly, or add the result to the project as a new sequence. The existing originals are unchanged. The junction report contains original input DNA, orientation, overlap choices and product coordinates. Changing settings or a source clears old output. Calculation is local and does not upload DNA or add telemetry.

Verification covers 88 independently constructed known-product cases and 1,314 feature extractions using Biopython 1.85, including pUC19 assemblies from two, three, five and eight fragments. These check DNA arithmetic and annotation mapping, not a lab reaction. The interactive two-fragment pUC19 example is made in silico from NCBI M77789.2 with two 20-base overlaps; it is not a validated PCR or cloning protocol.

Compare a read with its reference

Open your reference and sequencing read, then choose Compare sequences. Select which sequence is the reference, select the read and, if needed, narrow its range using one-based inclusive coordinates. The tool fits the entire selected read to the reference, checking both orientations by default. Circular references are searched across the origin; a result spanning more than one reference traversal is refused. A partial read leaves the remaining reference untested.

The local affine-gap algorithm scores an exact A/C/G/T match +2, mismatch −3, gap opening −5 and each subsequent gap base −1. Uncovered reference flanks are free; read-end gaps are penalized. Ambiguous nucleotide letters score 0 and never count as exact matches. The exact-match percentage divides definite matches by all alignment columns, including gaps and unresolved positions. Quality scores are shown for inspection, not used to weight alignment scores. The comparison has a 25-million-cell limit per orientation; trim the read or use a shorter reference when exceeded.

One best alignment is shown. Tied end placements or orientations are flagged, but repeats can also permit alternative gap placements within the same interval. Coordinates in the report refer to the original reference and the original untrimmed read; reverse read coordinates descend. Insertions are located between reference bases. Annotation names describe overlap or adjacency, including compound features; they are not predictions of protein effects. Scores are checked against 123 cases using Biopython 1.85 PairwiseAligner, including public pUC19 and AB1-derived sequences.

For AB1 reads, the comparison panel shows the original trace channels, base calls and available Phred qualities. A difference's read position opens the corresponding trace region. Trace display is unavailable when the current sequence no longer matches the original calls. Selecting a range changes the comparison and the optional trimmed FASTA download; it does not alter the original trace or project sequence. Download report saves the settings, placement, differences and aligned bases as text. Changing inputs or canceling discards a pending comparison.

Scope and sources

AB1 import displays the called sequence and available chromatogram data. Automatic quality trimming, multiple alignment, cloning workflows beyond the ordered overlap model above, 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.

The tests cover the cases described on this page; they do not certify every possible file or input. If you find a result that disagrees with an authoritative source, please report it to hello@plasmidmap.com with the inputs.

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