Capabilities

Keep sequence work together

Bring sequence records, annotations, primer sets and saved analyses into projects and folders.

The development build works with DNA and protein FASTA, GenBank/GBFF, SnapGene, EMBL and AB1 files. GFF3 and GTF annotations can be used with their corresponding sequence records.

Each tool has its own supported inputs and limits. Annotation-based operations need suitable annotations and matching sequence data.

Explore maps and annotations

Move between a whole-genome or plasmid view and the individual bases. Linear and circular maps keep annotated features in context while you search and inspect regions of interest.

SeqAtlas development view of a circular 4.63 Mbp genome, with coloured annotations, project folders and annotation-layer controls. — Development view Circular genome map and annotation layers.

The genome overview brings annotation density, sequence statistics and display layers into the same view. Optional layers distinguish genes, non-coding RNA, repeats and other features.

A closer look at gene structure

Zoomed views keep exon and intron structure aligned with the coordinate scale and strand direction.

SeqAtlas development detail showing two annotated gene models on opposite strands, with exon blocks and connecting introns aligned to genomic coordinates. — Development detail Gene structure along genomic coordinates. Scroll sideways to inspect the detail.

Work with regions, transcripts and proteins

Extract genomic regions or annotated coding sequences, choose transcripts and generate protein sequences from suitable bacterial and eukaryotic records.

Reverse-complement sequences, inspect translations and save edited constructs with their annotations. CDS and transcript results depend on the structure and completeness of the supplied annotations.

Plan a construct before the experiment

Review predicted fragments and assembled sequences before moving to the bench.

Restriction digests and ligation
PCR product previews
Gibson assembly
Golden Gate assembly

Inspect recognition sites, cut coordinates and sticky ends. Save fragments or assembled constructs while retaining their annotations.

Restriction sites marked around a 5,040 bp plasmid beside a list of enzymes, cut positions and overhangs in the earlier SeqAtlas browser interface. — Earlier browser interface Restriction sites, cut positions and overhangs.

Design primers in sequence context

Primer3-based tools support PCR and Gibson primer design. Add restriction-site tails, inspect binding sites and predicted products, then keep or export the selected primer sets.

Candidate forward and reverse primers mapped over hydN, with a selected PCR region highlighted in the earlier SeqAtlas browser interface. — Earlier browser interface Candidate primers and the highlighted PCR region.

Enlarged detail: candidate primer arrows and the selected PCR region. From the earlier SeqAtlas browser interface. — Enlarged detail: candidate primer arrows and the selected PCR region. Full image

Reading the example

The earlier browser view shows a primer pair above hydN, with the intended PCR region aligned to the sequence coordinates.

Predictions support experimental planning and require independent checks.

Search locally and compare sequences

Use local BLAST against genomic sequence, annotated CDS or translated proteins. Inspect matches on the map and compare DNA or protein pairs to examine differences.

Two nifH protein sequences aligned with differences highlighted and alignment statistics above, from the earlier SeqAtlas browser interface. — Earlier browser interface Pairwise protein alignment with differences highlighted.

This earlier browser example shows differences and alignment statistics for two protein sequences. Core search and comparison analyses run locally on the Mac.

Read chromatograms alongside a reference

Open AB1 traces to inspect called bases and quality information where it is available.

Check AB1 brings multiple reads into a reference comparison so you can examine discrepancies, covered regions and gaps. Save the analysis alongside the rest of the project.

Inspect CRISPR guide candidates

Identify candidate guides for SpCas9 and AsCas12a, inspect their sequence positions and compare them with local reference genomes for possible off-target matches.

SeqAtlas development detail showing guide candidates as arrows along genomic coordinates, a selected candidate and the annotated sequence below. — Development view Guide positions and a selected candidate on the sequence map. Scroll sideways to inspect the detail.

The selected candidate stays aligned with the coordinate scale and annotated sequence. Arrows show candidate positions and strand direction.

Optional SpCas9 activity estimates are based on sequence. Guide rankings and off-target searches are predictions with method and reference limits; they do not establish experimental activity or specificity.

Review and adapt codon choices

Inspect codon usage and optimise supported coding sequences against selected host tables while keeping the encoded protein unchanged.

Screen for selected restriction sites or sequence patterns and remove them within the supported optimisation workflow. The result still needs sequence and experimental validation.

Export results and preserve projects

A labelled E. coli sequence figure beside controls for its layout, labels and colours in the earlier SeqAtlas browser interface. — Earlier browser interface Sequence figure layout, labels and colours.

Export sequence records, annotations and analysis results. Create figures in editable SVG or PDF and PNG formats.

The pictured figure controls are from the earlier browser interface. Local backup and restore tools are part of the Mac project workflow.