Plasmid maps and sequences, always connected
The molecular work, beside the experiment.
Bring a sequence in by pasting it, fetching an accession from GenBank or UniProt, saving a BLAST hit, or importing FASTA, GenBank, and SnapGene files, several at a time. It opens on the view that suits it: the bases in rows, a linear feature map, or the circular plasmid map for a circular construct, with open reading frames and restriction sites drawn over the top.
Drag out a region and the tools open on those bases. Design primers or guide RNAs, translate, reverse complement, codon optimize for a host, or annotate what you found. A tool result saves back into the project with a record of where it came from, so a construct sits beside the samples it went into and the images it explains.
See the digest before you run it
Pick your enzymes and Restriction Digest shows the fragments and the gel they would make, at the agarose percentage that suits their sizes. The list says how many times each enzyme cuts this sequence, so a single cutter is visible before you choose it, and fragments close enough to run as one band are called out. Save the picture to sit beside the real photograph, or send it to a notebook page with a caption naming the enzymes and the percentage.
Get ranked guide RNAs for the region you picked
CRISPR Design opens on your selection, in a target region you can still widen or move, and finds guides against the PAM you choose within your GC bounds. Each one comes back ranked, carrying its protospacer, its PAM, the strand and position it sits at, and its GC content. Add the ones you want to the map as features.
Align sequences and read what changed
Multiple Alignment lines a sequence up with the others you pick, and Align in the bulk bar sends a whole selection straight into one. Matches, mismatches and gaps are marked base by base, with the score and percent identity above them. From the same set, build a UPGMA phylogenetic tree, download it as an SVG whose branches and tip labels stay editable, or copy it out as Newick.
Turn on the layers the question needs
Layers draw open reading frames in all six frames, restriction sites on both strands and aware of circularity, amino acids under coding features, and the complement strand. Select a stretch and the status bar reads back its coordinates, length, GC content, reading frame, and how many amino acids it encodes. Register the sequence and it takes a running identifier: PL-0001 for a plasmid, with ST-, OL-, AB- and CL- for strains, oligos, antibodies and cell lines.
More in the Genetics workspace
Getting sequences in
Import and fetch
FASTA, GenBank, and SnapGene .dna files, dragged on in batches, or an accession fetched from GenBank or UniProt with its annotations and topology.
BLAST
Search nucleotide, protein, or SwissProt. Saving a hit fetches the full annotated record by accession.
Search your library by sequence
Paste a sequence, FASTA or raw, and find everywhere it appears across your library, on either strand.
Design and analysis
Annotations, typed and colored
Gene, CDS, promoter, terminator, origin, primer binding site, and your own types, plus Auto-Detect for T7 promoters, resistance markers, reporters, origins, tags, and ribosome binding sites.
Primer design
Set primer length, melting-temperature range, product size, and salt concentration, then add the results to the map as labeled primer annotations.
Codon optimize
Rewrite a selection for a target organism and apply it in place, leaving the rest of the sequence as it was.
Construct assembly
Pick parts from your Part Library, reorder them, flip any one to its reverse complement, and save the result as a new sequence that records what it was built from.
Contig assembly
Assemble Sanger reads that carry quality scores.
Protein and RNA analysis
Hydropathy plot, protein properties including pI and extinction coefficient, secondary structure, and RNA secondary structure prediction.
Dotplot and sequence logo
Compare two sequences base by base, or read conservation across an alignment as information content.
Sharing and export
Connections
The construct a sequence was made from, anything made from it, and the samples and results it links to, recorded as you work.
Comments and sign-off
Comments anchored to a range of bases so feedback points at real bases, with @ mentions and approvals in the Activity panel.
Export
FASTA downloads, or Export Figure at a printed width in millimeters: SVG with every arrow, tick, and label a separate editable object, or PNG handed to the markup workspace.
Learn more: Manage sequences·Plasmid maps·Primer and CRISPR design·Restriction digest and cloning·File formats·vs. Benchling·vs. SnapGene
Import your first sequence
Draw its map, design against it, and keep what you find with the experiment. Free for you and one collaborator.