A FastAPI-based server for taxonomic annotation of DNA sequences.
- Upload FASTA files containing DNA sequences
- Run taxonomic annotation using BLAST or VSEARCH
- Track job status and retrieve results
- RESTful API with auto-generated documentation
- Python 3.14
- FastAPI 0.128
- BLAST+ 2.17
- VSEARCH 2.30
The results.json file contains taxonomic annotation results in a structured format.
The exact content depends on the tool used (BLAST or VSEARCH), but follows this general structure:
{
"results": [
{ ... }, # matches for each query sequence
{ ... },
...
],
"summary": {
"total_queries": 4,
"total_hits": 80
},
"metadata": {
"tool": "blast",
"algorithm": "megablast",
"database": {
"identifier": "eukaryome_its",
"version": "1.9.4"
},
"job_id": "job123"
}
}For each query sequence, the results are stored in the results array. For example:
{
"results": [
{
"query_id": "query_name",
"query_length": 553,
"hit_count": 2,
"hits": [
{
"sseqid": "EUK1101818;Fungi;Basidiomycota;Tremellomycetes;Filobasidiales;Piskurozymaceae;Solicoccozyma;aeria",
"taxonomy": {
"accession": "EUK1101818",
"kingdom": "Fungi",
"phylum": "Basidiomycota",
"class": "Tremellomycetes",
"order": "Filobasidiales",
"family": "Piskurozymaceae",
"genus": "Solicoccozyma",
"species": "aeria"
},
"pident": 100.0,
"length": 553,
"mismatch": 0,
"gapopen": 0,
"qstart": 1,
"qend": 553,
"sstart": 1235,
"send": 1787,
"evalue": 0.0,
"bitscore": 998.0,
"qcovs": 100.0,
"sstrand": "plus",
"slen": 4063,
"alignment": {
"qseq": "GTGGGATTAAA...", # truncated
"midline": "||| |||||...", # truncated
"sseq": "GTGAATTAAA..." # truncated
}
},
{ ... }, # other hits
]
},
{ ... }, # other query sequences
{ ... }
],
"summary": { ... },
"metadata": { ... }
}Each hit contains the following information:
- sseqid: Identifier of the reference sequence
- taxonomy: Taxonomic classification object with fields (accession, kingdom, phylum, class, order, family, genus, species)
- pident: Sequence identity percentage
- length: Length of the alignment in nucleotides
- mismatch: Number of mismatched positions
- gapopen: Number of gap openings in the alignment
- qcovs: Percentage of query covered by alignment
- evalue: E-value (not available for VSEARCH output)
- bitscore: Bit score (for VSEARCH, raw score is used)
- qstart and qend: Start and end positions in query
- sstart and send: Start and end positions in subject/target
- sstrand: Alignment strand (e.g., "plus" or "minus")
- slen: Length of the subject sequence
- alignment: Object containing aligned sequences with fields:
- qseq: Aligned portion of query sequence
- midline: Match representation between sequences
- sseq: Aligned portion of subject sequence