blast_search
Read-only
Search a sequence against NCBI BLAST+ at EMBL-EBI (blastn, blastp, blastx, tblastn or tblastx) over ENA, UniProtKB, PDB and the vector-screening sets.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| No | EBI requires a contact address on every submission (their abuse contact, not a login). Left empty, the one saved in any EMBL-EBI panel is used. | ||
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| region | No | which part of the open record to search, when no sequence is wired in. Values: whole (the whole record), selection (the current selection), feature (a named feature). | whole |
| feature | No | the feature's name, matched case-insensitively on the open record. Only applies when region is feature. | |
| program | No | which BLAST program. The QUERY alphabet is derived from it and never asked for: blastx takes DNA and searches protein, tblastn the reverse. Values: blastn (blastn · dna query), blastp (blastp · protein query), blastx (blastx · dna query), tblastn (tblastn · protein query), tblastx (tblastx · dna query). | blastn |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| sequence | No | the query. Wire a record or a sequence output, or paste raw/FASTA. Left empty, the region below is taken from the open record. | |
| databases | No | database ids to search, as the service names them (em_rel, uniprotkb, pdb, emvec…). Several are searched together. Left empty, the service's OWN default for this program's context is used and reported back. | |
| parameters | No | every other advertised parameter, one `id=value` per line, using the service's own ids (exp, matrix, filter, gapopen, gapext, wordsize, alignments, scores, taxids…). Left empty each keeps the service's default for this context. An id the service does not advertise is refused by name rather than dropped. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| hits | Yes | every hit, with its HSPs, accession, organism and the links the service sent | |
| jobId | Yes | the dispatcher job id: what a methods section cites and what re-fetches this exact result | |
| topHit | Yes | the best hit by E-value: what a "what is this?" step reads | |
| tabular | Yes | the hits as BLAST's own outfmt 6 table, for download or a downstream parser | |
| hitCount | Yes | how many subjects matched | |
| sequences | Yes | the hit subjects as FASTA, ready to wire straight into an alignment or a tree | |
| topExpect | Yes | the best hit's E-value; wire into a $when to branch on significance | |
| provenance | Yes | the binary, the command line EBI ran, the databases as built, and the search space the E-values are relative to | |
| topCoverage | Yes | what fraction of the query the best hit covers, 0–1 | |
| topIdentity | Yes | percent identity of the best hit's best HSP |