Manage Genetic Sequences
Genetics is where DNA, RNA, and protein sequences live: imported or fetched, annotated, analyzed, and kept as a library your whole project can reach. It covers the everyday molecular biology work, from reading a plasmid map to designing primers and planning a digest.
Adding a Sequence
New sequence asks how you want to add one:
| Method | What it does |
|---|---|
| Paste Sequence | Paste raw sequence or FASTA text |
| GenBank | Fetch a record by accession number from NCBI |
| UniProt | Fetch a protein by accession |
| BLAST Search | Search for similar sequences and save a hit |
| Import File | Upload FASTA or GenBank files from your computer |
Pasting lets you set the sequence type or leave it on Auto-detect, and the input is filtered to the alphabet of whichever type is selected, so a protein pasted while DNA is chosen loses its residues rather than becoming nonsense.
A GenBank fetch brings the record's annotations with it, and its topology, which is what makes a circular plasmid open on the plasmid map rather than as a line.
Import File takes .fasta, .fa, .fna, .ffn, .faa, .frn, .gb, .gbk, .gbff, and .genbank, several at a time and several records per file. You can also drag files straight onto the workspace, which imports the batch with a progress count. Binary SnapGene files aren't supported.
BLAST
BLAST Search takes a query sequence, a database (nucleotide, protein, or SwissProt), and how many hits you want back. The right BLAST program is chosen from the sequence itself. Saving a hit fetches the full record by accession, so what lands in your library is the real annotated sequence rather than an alignment fragment.
Sequence lookups go straight from your browser to NCBI and UniProt. That's deliberate and it's disclosed on every screen that does it. For a fetch, the accession you typed is sent, and for BLAST the whole query sequence is. Nothing else from your project goes with it, no account, project, or contact details. Avoid searching sequences you need to keep unpublished.
The Viewer
A sequence opens in one of three views, switched from Views in the sidebar:
- Sequence View, the default, showing the bases themselves in rows with a ruler and annotation tracks
- Linear Map, the whole sequence as a feature map
- Plasmid Map, the circular view, which appears for circular non-protein sequences
Layers overlays computed information on top:
| Layer | Default | Notes |
|---|---|---|
| ORFs | On | Open reading frames in all six frames, labelled with their length |
| Restriction sites | On | Common enzymes, both strands, aware of circularity |
| Translation | Off | Amino acids under coding features, and not available on the plasmid map |
| Complement | Off | The reverse strand, and not available on the plasmid map |
On a large plasmid the ORF and restriction scans finish a moment after the sequence draws, so those layers appear slightly after everything else.
Select a region by dragging and the status bar tells you its coordinates, length, GC content, reading frame, and, when the selection divides by three, how many amino acids it encodes.
Cmd/Ctrl + F searches within the sequence and Cmd/Ctrl + G jumps to a position. Cmd/Ctrl + Z undoes.
The Selection Menu
Dragging out a region opens a menu, and this is the most important thing to know about the workspace: several tools live here and nowhere else.
- Create: Add Annotation, Save as New Sequence, and Design Primers
- Transform: Reverse Complement, Complement, Translate, Transcribe, and Reverse Transcribe
- Analyze: BLAST, Codon Optimize, CRISPR Design, and Find ORFs
- Plus Copy Sequence, and Comment on selection to anchor a discussion to those bases
Save as New Sequence asks you to name the region before it writes anything, then tells you it saved. From there you can Open sequence, or Keep working here to stay on the one you were reading.
Transforms open their result in a panel with the option to save it as a new sequence, so nothing overwrites your original unless you ask.
Design Primers takes a target region, primer length, melting-temperature range, product size, and salt concentration, and its results can be added to the map as labelled primer annotations. CRISPR Design finds guides against a PAM you choose within your GC bounds, and can add them to the map as features. Codon Optimize rewrites for a target organism, and applying it replaces the sequence in place.
Annotations
Add Annotation names a region and gives it a type: gene, CDS, promoter, terminator, origin, primer binding site, restriction site, a generic feature, or a custom one. Each type has its own color on the map.
Auto-Detect inside that dialog box scans a DNA sequence against a library of common parts (T7 promoter, resistance markers, reporters, origins, tags, ribosome binding sites) and annotates what it recognizes, which saves a lot of typing on a construct built from standard pieces.
The sidebar lists every annotation, with per-feature visibility toggles and hover highlighting into the map.
Analysis Tools
The sidebar's Analysis section holds the tools that work on the whole sequence:
- Multiple Alignment aligns this sequence with others you pick
- Translate Frames shows all three reading frames
- RNA Structure predicts secondary structure for RNA
- Hydropathy Plot, Protein Properties (pI, extinction coefficient, and more), and Secondary Structure for proteins
- Phylogenetic Tree builds a UPGMA tree from selected sequences, downloads it as an SVG whose branches and tip labels stay editable, and copies out Newick
- Dotplot and Sequence Logo
- Export Figure writes the map you are looking at, as an SVG or a PNG, at a printed width in millimetres
Assembly and Cloning
Construct Assembly builds a construct from parts you pick. Add parts opens the Part Library, where you search your sequences and tick the ones you want, and they land on the canvas in the order they were listed. Reorder them, flip any one to its reverse complement, and save the result as a new sequence, which records what it was assembled from.
Restriction Digest simulates a digest and shows the gel. Every enzyme in the list says how many times it cuts this sequence, so you can see a single cutter before you pick it, and Single cutters only narrows the list to those (anything you have already selected stays listed). Tick your enzymes to see the fragments, then View Gel.
The gel runs at an agarose percentage from 0.8 to 3.0, and the one that suits your fragment sizes is chosen for you and marked in the list. Hover a band to read its size. Where two fragments are close enough to run together, Conspecta says so, because on the real gel they will look like one band. The uncut lane shows what you would actually load: a circular plasmid runs as a bright supercoiled band ahead of its length and a faint nicked band behind it, not a single band at the sequence length. Save image downloads the gel as a picture you can put beside the real photograph, and Send to notebook puts it straight onto a page you pick, added at the end with a caption naming the enzymes and the percentage. The toast that confirms it has an Open link that takes you to the page at the new figure.
Contig Assembly assembles Sanger reads that carry quality scores.
The Registry
Register Item turns a sequence into a cataloged entity with an auto-incrementing identifier: a plasmid (PL-0001), strain (ST-), oligonucleotide (OL-), antibody (AB-), or cell line (CL-). Each type asks for the fields that matter for it, so a plasmid records its backbone, resistance marker, copy number, and promoter.
Opening the tool again on a registered sequence gives you Edit Registration, where you can correct those fields. The identifier is built from the entity type, so the type stays fixed once it is assigned. Unregister releases the identifier and clears the type's fields, which is how you register a sequence under a different type.
Registry on the sequences landing opens the whole catalog at once. Search by name or by identifier such as PL-0001, use the filter button to narrow to one entity type, then click an entry to open it. Only registered sequences appear, which is what separates it from the search on the landing itself.
Connections shows what a sequence is related to: the construct it was made from, anything made from it, and the samples and analysis it is linked to. Saving a tool result, a BLAST hit, or an assembly records where it came from automatically, so the trail builds itself as you work. Clicking a node re-centers the map on it, and its menu opens it, links from it, or removes the link.
Organizing
Sort by date, name, sequence type, or approval status, and filter by type, owner, modification date, or approval. Folders, stars, and the bulk bar work as they do elsewhere, and Align in the bulk bar sends a selection straight into a multiple alignment.
The toolbar also has a sequence search across your whole library: paste a sequence, in FASTA or raw, and Conspecta finds where it appears in anything you have, on either strand. That's how you find out whether you've already got the insert you're about to order.
A sequence carries an Activity panel with comments, @ mentions, and sign-offs, and a comment can be anchored to a specific range so feedback points at real bases.
Exporting
Download, from a sequence's menu or the bulk bar, writes FASTA.
Export Figure writes the map currently on screen — circular, linear, or the sequence rows — asking for a Width the way a journal does, in millimetres, and a Resolution.
Choose SVG and the map is drawn rather than photographed: feature arrows, the backbone, tick marks and every label arrive as separate objects, and the feature names stay text you can retype. Open it in Illustrator or Inkscape and recolour one feature without touching the rest.
Choose PNG and the map is captured as a picture, then handed to the markup workspace, where you can draw arrows and labels on it before downloading.