Interactively Search a Namespace

This endpoint searches the given namespace for alignments, given a query sequence, and returns these alignments.

HTTP Request

POST http://example.com/namespace/<ID>/search

URL Parameters

Parameter	Description
ID	The unique identifier for the namespace to search for alignments

Query Parameters

Parameter	Description
file	A FASTA file containing a query sequence for which alignments are sought in the given namespace
sequence	A string containing a query sequence (as an alternative to file)
offset	An optional 0-based index from which to start retrieving results (default: 0)
N	The maximum number of results to retrieve (default: retrieves all results)
eVal	The maximum E-Value threshold for the search (default: none)
maxHits	The number of results after which the search immediately returns (default: no max)

Response

{
  "impl":"last",
  "alignments":[
    {
      "queryid":"VIOA_CHRVO",
      "queryalignseq":"MKHSSDICI...",
      "querylenseq":418,
      "queryalignstart":0,
      "targetid":"UniRef50_Q9S3V1",
      "targetalignseq":"MKHSSDICI...",
      "targetlenseq":418,
      "targetalignstart":0,
      "bitscore":983,
      "evalue":1.9e-320
    },
    {
      "queryid":"VIOA_CHRVO",
      "queryalignseq":"MKHSSDICI...",
      "querylenseq":418,
      "queryalignstart":0,
      "targetid":"UniRef50_A0A1E7VPW7",
      "targetalignseq":"MTNYSDICI...",
      "targetlenseq":448,
      "targetalignstart":13,
      "bitscore":507,"evalue":1.1e-153
    },
    ...
  ],
  "namespaces":[
    {
      "id":"uniref50","desc":"The UniRef 50 database",
      "datasource":"UniProt",
      "database":"uniref50",
      "lastmod":1537919196,
      "seqcount":10000
    },
  ]
}

Examples

curl -F file=@sequence_fasta_file http://example.com/namespace/<ID>/search

The above command returns a JSON object containing data for any alignments found for the query sequence against the target namespace, as well as metadata for the given namespace.

curl -F sequence=sequence_string -F maxHits=10 http://example.com/namespace/<ID>/search

The above command returns a JSON object containing data for any alignments found for the query sequence given by the sequence parameter, limiting the search to at most 10 alignments.