ebi_align
Read-only
Run a sequence through EMBL-EBI's Job Dispatcher: Clustal Omega, MUSCLE, MAFFT, Kalign, T-Coffee, EMBOSS needle/water/matcher/stretcher, LALIGN, phmmer, hmmscan, PSI-BLAST or Phobius.
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. | ||
| stype | No | query alphabet, where the service takes one. Values: dna (nucleotide), protein (protein). | dna |
| _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. | |
| service | No | which EBI service to run. Values: clustalo (Clustal Omega — HMM-profile progressive MSA), muscle (MUSCLE — Iterative refinement MSA), mafft (MAFFT — FFT-based progressive/iterative MSA), kalign (Kalign — Wu-Manber approximate-string-matching MSA), tcoffee (T-Coffee — Consistency-based MSA), emboss_needle (EMBOSS needle — Needleman–Wunsch GLOBAL pairwise alignment: end-to-end, the whole of both sequences.), emboss_water (EMBOSS water — Smith–Waterman LOCAL pairwise alignment: the best-matching subregion, ignoring the rest.), emboss_matcher (EMBOSS matcher — Waterman–Eggert local pairwise alignment, like water, but it can report several alternative non-overlapping local alignments instead of only the single best one.), emboss_stretcher (EMBOSS stretcher — Myers–Miller GLOBAL pairwise alignment in linear space: the same answer needle gives, on sequence pairs too long for needle to hold in memory.), lalign (LALIGN — Huang & Miller), hmmer3_phmmer (HMMER phmmer — Profile HMM search of one protein against a protein database), hmmer3_hmmscan (HMMER hmmscan — Search ONE protein against a profile-HMM library), psiblast (PSI-BLAST — Position-Specific Iterated BLAST: it builds a profile from the hits of one round and searches again with it, which finds remote homologues plain blastp misses.), phobius (Phobius — Combined signal-peptide and transmembrane-topology prediction: the two are modeled together, so a signal peptide is not miscalled as a TM helix.), radar (RADAR — Rapid Automatic Detection and Alignment of Repeats: finds a protein’s INTERNAL repeats and aligns the copies against each other, without a library to match them to.), pratt (Pratt — Pattern discovery). | clustalo |
| _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. | |
| sequences | No | the sequences to align. Wire records or sequence outputs, or paste FASTA. Multiple-alignment services take all of them; a pairwise service takes exactly two. | |
| parameters | No | every other parameter the chosen service advertises, one `id=value` per line, using its own ids (matrix, gapopen, gapext, format, iterations…). Left empty each keeps the service's default. An id the service does not advertise is refused by name rather than dropped, and so is a value outside the list it publishes for this alphabet. | |
| include_subject | No | include the record this step is running on as the first sequence. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| raw | Yes | the native text the service returned, for download | |
| hits | Yes | the PSI-BLAST hit table, in the same shape blast_search hands downstream | |
| rows | Yes | the aligned rows as plain strings, ready to wire into build_tree or a scorer | |
| jobId | Yes | the dispatcher job id: what a methods section cites and what re-fetches this exact result | |
| local | Yes | LALIGN’s non-overlapping local alignments, each with its own score, E-value and spans | |
| newick | Yes | the service's own guide tree, ready for the Phylogenetics tool | |
| repeats | Yes | RADAR’s internal repeat families, each copy with its residue span and its two scores | |
| identity | Yes | the percent-identity matrix the service computed | |
| pairwise | Yes | the pairwise report (needle/water/matcher/stretcher) | |
| patterns | Yes | Pratt’s discovered patterns in PROSITE notation, each with where it matched in every sequence | |
| topology | Yes | the Phobius signal-peptide and transmembrane features, with their spans | |
| alignment | Yes | the aligned sequences (multiple-alignment services) | |
| profileHits | Yes | the HMMER hits (phmmer, hmmscan) with their domains and inclusion thresholds |