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Importing sequences

Every way to get data into deoxy (local files, accessions, and gene symbols), the supported formats, and how deoxy automatically decides whether a file becomes a sequence, a genome, an alignment, or a group.

8 min read

Three ways to import

Open the importer with + → Import from the nav rail. The modal has three lanes across the top.

From your computer
Drop a file onto the zone or pick one. Accepts FASTA, GenBank, EMBL, SnapGene .dna, AB1 chromatograms, and Newick trees.
By accession
Paste an accession (e.g. NC_000913, P69905, LR699001) and pick a source: Auto-detect, NCBI, ENA, or UniProt. Click Look up to preview before importing.
By gene symbol (Ensembl)
Choose a Species (Human, Mouse, and Rat are pinned) and enter a gene symbol or stable ID such as BRCA1 or ENSG00000012048.

Every lane also offers an optional Labels picker (deoxy suggests labels from the organism and title) and, for nucleotide previews, a Topology choice of Linear or Circular, unless the file format already declares its topology.

Supported file formats

FASTA (.fasta, .fa, .fna, .fsa, .ffn, .faa)
Single record → a DNA or protein sequence (deoxy detects which from the residues). Multiple records → an alignment or a group (see routing below).
GenBank (.gb, .gbk, .gbff, .genbank)
Sequence plus its features and annotations. Topology and DNA-vs-protein come from the LOCUS line.
EMBL (.embl)
Sequence plus features, like GenBank.
SnapGene (.dna)
Sequence, topology, and features. (Primers stored in .dna files are not imported yet.)
AB1 (.ab1)
A Sanger trace that imports as a DNA sequence with its chromatogram, viewable via the Chromatogram layer.
Newick (.nwk, .newick, .tree)
A phylogenetic tree (needs at least two leaves).
CSV annotations / primers
Not imported from this modal. Add them to an open document from the Annotations tab (Import CSV) or the Primers tab (Import…).

How deoxy decides what your file becomes

This is the part that feels like magic but is actually a few clear rules. Knowing them tells you exactly what you will get.

  1. Small single record → a sequenceA FASTA/GenBank/EMBL file with one record under 100,000 bp opens as an ordinary DNA or protein document.
  2. Large single record → a streamed genomeOne record over 100,000 bp routes to Import genome from file. Genomes load only the region you are viewing, so chromosome-scale sequences stay fast. The fallback button Import as sequence (first 100k bp) truncates instead, if you only need the start.
  3. Multiple equal-length records with gaps → an alignmentIf every record is the same length and gap characters are present, the file is treated as a multiple-sequence alignment (MSA).
  4. Multiple equal-length records, no gaps → you choosedeoxy cannot tell whether equal-length, gap-free records are an alignment or just a set of equal sequences, so it asks. Answer msa for an alignment or group for a sequence group.
  5. Multiple unequal-length records → a groupRecords of differing lengths become a group document, a stack of independent sequences you can edit, reorder, and analyze row by row.

The same routing runs whether you import a file, paste, or drop it onto the editor. Accession and gene-symbol imports follow the size rule too: a nucleotide record over 100,000 bp shows an Import as genome button instead of Import.

Importing a group of sequences directly

When you already know you want a group, skip the routing and use the dedicated lane.

  1. Open the group importerClick + → Import group.
  2. Add your sequencesDrop one or more .fa, .fasta, .fna, .faa, .ab1, or .seq files, or a single .zip containing them.
  3. Work with the resultThe group opens as a stacked editor. Each row keeps its own label, ruler, sequence, and (for AB1) chromatogram, and you can rename, reorder, delete, or open any row as its own document.

Size limits

Single uploads are capped at 50 MB on the current tier. For large alignments, filter to fewer sequences or trim columns before importing; for large genomes, the streamed genome path keeps memory bounded regardless of total length. Larger uploads arrive with the paid tier.

Migrating from another tool

Coming from Benchling, Geneious, or SnapGene? deoxy imports GenBank, FASTA, EMBL, SnapGene .dna, AB1 traces, and Newick trees today, and you can export back out anytime. Benchling export is on the roadmap.

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