Schemas

Every sub-expression must hold.

Which vocabulary value comes from.

A Pfam accession (e.g. 'PF00069') or Rfam accession (e.g. 'RF00174') as a string, or an SAE feature id (e.g. 8581) as an integer. Valid values are listed by /api/v1/pfam-families, /api/v1/rfam-families and /api/v1/sae-features.

The sub-expression to negate.

At least one sub-expression must hold.

Every sub-expression must hold.

A Pfam accession, e.g. 'PF00005'. See /api/v1/pfam-families.

The sub-expression to negate.

At least one sub-expression must hold.

Short summary of the problem type, e.g. 'Unprocessable Entity'.

Repeats the HTTP status code.

Explanation specific to this occurrence.

Identifier for this error. Include it when reporting a problem.

Field-level failures. Present on validation errors (422).

What was wrong, e.g. 'Input should be a valid integer'.

Dotted path to the offending field, e.g. 'body.sequences.0'.

Machine-readable error code, e.g. 'string_type' or 'missing'.

The value that was rejected, echoed back.

Optional label for this query, returned as queryId in matchIndices. Must be unique within the request.

Pfam domains that the protein matched by this query must have, as a single accession or combined with and, or and not. See /api/v1/pfam-families.

The closest SwissProt match for each input sequence, in the order the sequences were sent.

Percent identity between this protein and its SwissProt match (id). This describes the annotation, not the search match. Null if not available.

Percent of this protein covered by the alignment to its SwissProt match. Null if not available.

Sample (genome) the gene is in.

Contig the gene is on.

Gene identifier, unique within its contig. The same identifier appears in gene IDs exported from the SeqHub website.

Strand the gene is on, "+" or "-".

Gene start position (bp) on the contig, inclusive.

Gene end position (bp) on the contig, inclusive.

Protein sequences to annotate (each max length 15000). Maximum 128 sequences.

The match's sampleId.

The match's contigId.

Position on the contig, 1-based and inclusive.

Position on the contig, 1-based and inclusive.

DNA for the range, always on the plus strand.

Pfam accession, e.g. 'PF00069'.

Pfam family name, e.g. 'Pkinase'.

Domain start position within the protein sequence (1-based).

Domain end position within the protein sequence (1-based, inclusive).

Pfam family description, e.g. 'Protein kinase domain'.

hmmsearch bitscore for this domain hit.

hmmsearch E-value for this domain hit.

Domain start position (bp) on the contig, inclusive.

Domain end position (bp) on the contig, inclusive.

Index into this match's contig array.

Which entry of the request's sequences this protein matched, 0-indexed.

The query's id, or null if none was given.

Percent identity of the blastp alignment between the query and the matched protein. Null if blastp found no alignment.

Percent of the query sequence covered by the blastp alignment. Null if blastp found no alignment.

Sample of the contig this match is on. Use with contigId to fetch DNA from /api/v1/contig-dna.

Contig this match is on. See sampleId.

One entry per query: sequences[queryIndex] matched contig[contigProteinIndex].

SAE features in the window. By default, only those named in featureFilter; set includeOtherSaes to return all of them.

Rfam families found in the window, each with its hits. By default, only families named in featureFilter; set includeOtherRfams to return all of them.

1-5 protein sequences to search for (each max 15000 characters). Standard 20 and ambiguous B, X, Z, U residues are allowed.

Either all plain sequence strings, or all ProteinQuery objects. A ProteinQuery adds an optional id and an optional pfamFilter on the protein that query matches.

Only return matches whose window satisfies this expression of Pfam, Rfam and SAE features, combined with and, or and not. At most 25 features. Valid identifiers are listed by /api/v1/pfam-families, /api/v1/rfam-families and /api/v1/sae-features.

Only return matches from genomes matching this taxonomy expression: a single {rank, value}, or several combined with and, or and not. At most 10 taxa. See /api/v1/taxa.

How diverse the results are. Higher levels search only one representative protein per cluster of similar sequences, so near-identical proteins don't crowd out the results. low (default): clusters at 90% identity, returning the most similar results. medium: 70% identity. high: 50% identity. max: 30% identity, the most diverse results. For distant homologs, use high or max: at low, results can fill up with near-identical close matches.

Maximum number of results to return, up to 100.

Also return every SAE feature in each match's window, not just those named in featureFilter. Makes the response much larger.

Also return every Rfam hit in each match's window, not just those named in featureFilter.

Genomic neighborhoods where every query sequence found a match, best first.

The protein sequence to search for (max length 15000). Standard 20 and ambiguous B, X, Z, U residues are allowed.

Only return matches from genomes matching this taxonomy expression: a single {rank, value}, or several combined with and, or and not. At most 10 taxa. See /api/v1/taxa.

How diverse the results are. Higher levels search only one representative protein per cluster of similar sequences, so near-identical proteins don't crowd out the results. low (default): clusters at 90% identity, returning the most similar results. medium: 70% identity. high: 50% identity. max: 30% identity, the most diverse results. For distant homologs, use high or max: at low, results can fill up with near-identical close matches.

Maximum number of results to return, up to 100.

Genomic neighborhoods around the closest matches to the query sequence, most similar first.

Rfam accession, e.g. "RF00174". See /api/v1/rfam-families.

Hits within the returned window.

Highest nhmmer score among this accession's hits in the window.

Start position (bp) of the hit on the contig, inclusive.

End position (bp) of the hit on the contig, inclusive.

Strand the hit is on, "+" or "-".

Rfam family name, e.g. "Cobalamin".

Rfam accession, e.g. "RF00174".

nhmmer E-value for this hit.

nhmmer bit score for this hit.

SAE feature id. See /api/v1/sae-features.

Where the feature fires within the returned window.

Number of positions in the window where the feature fires. Can be less than the total length of runs, since a run may include short gaps.

Start position (bp) of the run on the contig, inclusive.

End position (bp) of the run on the contig, inclusive.

Strand the run is on, "+" or "-".

Peak activation among the run's firing positions.

Positions within the run where the feature fires, as bp offsets from start. A run may include short gaps, so use these for exact positions. May be absent.

Index into contig of the protein that matched the query sequence.

Sample of the contig this match is on. Use with contigId to fetch DNA from /api/v1/contig-dna.

Contig this match is on. See sampleId.

Percent identity of the blastp alignment between the query and the matched protein. Null if blastp found no alignment.

Percent of the query sequence covered by the blastp alignment. Null if blastp found no alignment.

Stable identifier of the contig segment this match is on.

The proteins in the matched window.

Rfam families found in the window, each with its hits. By default, only families named in featureFilter; set includeOtherRfams to return all of them.

SAE features in the window. By default, only those named in featureFilter; set includeOtherSaes to return all of them.

Sample of the contig this match is on. Use with contigId to fetch DNA from /api/v1/contig-dna.

Contig this match is on. See sampleId.

The features that must occur together: Pfam, Rfam and SAE feature literals combined with and, or and not. At most 10 literals. The expression must always require at least one feature to be present, so an expression that can be satisfied by not terms alone is rejected. Valid identifiers are listed by /api/v1/pfam-families, /api/v1/rfam-families and /api/v1/sae-features.

Only return matches from genomes matching this taxonomy expression. See /api/v1/taxa.

Window radius in genes (not base pairs) around each feature hit. Required features must fall within this window, and the proteins in it are returned. At most 20.

Return at most one match per taxon at this rank, so results are not dominated by over-represented lineages. Set to null to return every match.

Maximum number of results to return, up to 100.

Also return SAE features in the window that are not named in featureFilter. Makes the response much larger.

Also return Rfam hits in the window for families not named in featureFilter.

Genomic neighborhoods where the feature expression is satisfied.

Every sub-expression must hold.

One of the seven ranks, e.g. 'genus'.

A taxon name at that rank, e.g. 'Escherichia'. See /api/v1/taxa.

The sub-expression to negate.

At least one sub-expression must hold.