Contig DNA

Fetch Contig DNA

POST

https://api.seqhub.org

/api/v1/contig-dna

Fetch DNA for up to 100 ranges on contigs returned by a search. Identify the contig with a match's sampleId and contigId, and give 1-based inclusive start/end coordinates. Any start/end in a search response works: a gene's cdsId, a Pfam domain, an Rfam hit or an SAE run.

Sequences are always returned on the plus strand, so reverse-complement minus-strand features yourself. If any range is invalid, for example past the end of its contig, the whole request fails.

Fetch Contig DNA › Request Body

ContigDnaRequest

ContigDnaRange[] · minItems: 1 · maxItems: 100 · required

Fetch Contig DNA › Responses

Successful Response

ContigDnaResponse

ContigDnaSequence[] · required

POST/api/v1/contig-dna

curl https://api.seqhub.org/api/v1/contig-dna \
  --request POST \
  --header 'Content-Type: application/json' \
  --header 'Authorization: Bearer <token>' \
  --data '{
  "ranges": [
    {
      "sampleId": "2799112551",
      "contigId": "Ga0313777_1080",
      "start": 6622,
      "end": 6632
    },
    {
      "sampleId": "2799112551",
      "contigId": "Ga0313777_1080",
      "start": 1381,
      "end": 3735
    }
  ]
}'

Example Request Body

{
  "ranges": [
    {
      "sampleId": "2799112551",
      "contigId": "Ga0313777_1080",
      "start": 6622,
      "end": 6632
    },
    {
      "sampleId": "2799112551",
      "contigId": "Ga0313777_1080",
      "start": 1381,
      "end": 3735
    }
  ]
}

json

Both ranges come from the feature context search example: the SAE feature's run (6622-6632), and the whole window from the first protein's start to the last protein's end (1381-3735).

application/json

Example Responses

{
  "sequences": [
    {
      "sampleId": "2799112551",
      "contigId": "Ga0313777_1080",
      "start": 6622,
      "end": 6632,
      "sequence": "ATGCGTTACGA"
    },
    {
      "sampleId": "2799112551",
      "contigId": "Ga0313777_1080",
      "start": 1381,
      "end": 3735,
      "sequence": "ATGAATTATCCGCTGACGCTGGAACAGTAT..."
    }
  ]
}