Files & formats

GFF3 annotation parser

Read a GFF3 annotation file: every feature with its 1-based inclusive coordinates, strand, phase, score and decoded attributes, plus any sequences from an embedded ##FASTA section. GFF3 usually carries NO sequence — it annotates a separate FASTA, joined on the first column — so the result says which of the two it was handed. Give sequence (or let an embedded ##FASTA supply it) to also get the record as GenBank, readable by every other tool here. Percent-escapes are decoded, . is read as absent rather than zero, and a feature repeated across lines keeps both lines.

post/parse_gff3

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/parse_gff3
  • Auth: none required

Request body

textstring required

GFF3 text. Up to 200,000 feature lines.

seqidstring

Which sequence's features to return, when the file covers several. Defaults to the first.

sequencestring

The DNA these annotations describe, when the file has no ##FASTA section. Enables the GenBank output.

asGenbankboolean

Also return the record as a GenBank flat file, when a sequence is available.

limitinteger

Most features to return in the table (1-5000).

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.