io.github.genmnz/jean

• sourcestringrequired“what this lane holds.”
• detailstring“for a ladder: its name; for a digest: comma-separated enzymes.”
• product_bpnumber“for a pcr lane: the product length, e.g.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• lanesarrayrequired“the lanes, each {name, lengths: [bp, …]}.”
• ladderstring“the MW marker in the reference lane, which is also the curve every lane's migration is read off unless `agarose_percent` is set.”
• agarose_percentnumber“the gel's agarose (% w/v).”
• mobility_modelstring“which published mobility law the agarose % is applied through.”
• dna_formstring“topology of the sample DNA: supercoiled and nicked circles do not migrate where a linear fragment of the same length does.”
• stainstring“the dye the plate was stained with; its published emission maximum is the colour the bands are drawn in.”
• exposurestring“Whole plate: brightness against the brightest band on the plate (a lightly loaded lane, the ladder included, can draw almost black); Per lane: brightness again…”
• lane_widthnumber“how wide each lane is drawn.”
• labelsboolean“print the ladder's readable bp marks, each lane's number above its well and a legend naming it.”
• captionboolean“the line under the plate naming the curve that positioned the bands and what their brightness is relative to.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• primerstringrequired“primer sequence 5'→3'.”
• thresholdsobject“the identity boundaries the ✓/⚠/~/✗ verdict is cut at.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• oligosarrayrequired“the oligos to lay out, 5'→3'.”
• namesarrayrequired“a name per oligo, in the same order.”
• formatnumber“wells per plate.”
• fillstring“how the plate is loaded.”
• plate_namestring“the plate's name, which becomes the worksheet's name.”
• mixedboolean“one well per PRIMER PAIR: `oligos` is read as forward, reverse, forward, reverse, and each plate is written as every well once carrying the forwards and again …”
• pad_to_capacityboolean“write every unused well as the supplier's blank-name, blank-sequence row rather than ending the sheet short.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• genbankstringrequired“the record to submit, as GenBank text.”
• collection_datestring“when the sample was collected.”
• geo_loc_namestring“where the sample came from: a country, ocean or sea from the INSDC vocabulary, optionally `:region` and `, locality`.”
• organismstring“the scientific name of the source organism.”
• mol_typestring“one of INSDC's two MANDATORY qualifiers on the source key.”
• topologystring“circular for a plasmid.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• genbankstringrequired“the record to submit, as GenBank text.”
• studystring“the Webin Portal study accession (PRJEB… or ERP…).”
• descriptionstring“the DE line, what the sequence is.”
• collection_datestring“when the sample was collected, on the source feature.”
• geo_loc_namestring“where the sample came from, from the INSDC vocabulary, or a missing-value term.”
• organismstring“the scientific name of the source organism; ENA checks it against its taxonomy.”
• mol_typestring“the source feature's mandatory /mol_type.”
• topologystring“circular for a plasmid (the ID line; only then may a feature cross the origin).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• oligosarrayrequired“the oligos to screen, 5'→3'.”
• namesarray“optional labels, in the same order as `oligos` — what the pair table calls each one.”
• mv_concnumber“monovalent cations (Na⁺ + K⁺ + Tris⁺), mM.”
• dv_concnumber“divalent cations (Mg²⁺), mM.”
• dntp_concnumber“total dNTPs, mM — subtracted from the divalent term, because dNTPs chelate Mg²⁺.”
• dna_concnumber“oligo strand concentration, nM — it moves a DIMER's Tm and leaves a hairpin's alone, because a hairpin is unimolecular.”
• temperaturenumber“the temperature ΔG is evaluated at.”
• max_loopnumber“largest internal loop the alignment will span (primer3's MAX_LOOP).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• vendorstring“which vendor product to measure against.”
• sequencestring“the sequence to measure.”
• featurestring“measure a named feature of the open record instead of the whole thing — the insert you are about to order rather than the vector it sits in.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• readstringrequired“the read's bases — wire a trace reader's `sequence` output here, or paste them.”
• referencestring“what to align against.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• readsstringrequired“the reads to trim, as FASTQ - quality lines are required, because both halves of this need them.”
• adapterstring“the adapter sequence to remove.”
• adapter_kindstring“which end the adapter sits at.”
• quality_cutoff_backnumber“quality cutoff for the 3' end, where quality decays with cycle number.”
• quality_cutoff_frontnumber“quality cutoff for the 5' end, which fails for different reasons than the 3' end and so takes its own number.”
• max_error_ratenumber“errors allowed in the adapter match, as a fraction of the overlap.”
• min_overlapnumber“an adapter overlap shorter than this is ignored.”
• min_lengthnumber“reads shorter than this after trimming are COUNTED as too short, not removed - this tool does not filter.”
• phred_offsetnumber“quality encoding: 33 for every modern FASTQ, 64 only for pre-1.8 Illumina.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• readsstringrequired“the reads, as FASTQ: four lines per record, quality line required.”
• groupingstring“how read positions pool into one group: FastQC's default (the first 9 bases one by one, then groups sized to stay under 75), none (one per base, --nogroup) or …”
• phred_offsetnumber“quality encoding: 33 for every modern FASTQ, 64 only for pre-1.8 Illumina (FastQC's --phred64).”
• adaptersstring“adapters to search for, in FastQC's --adapters format (a name, a tab, a sequence, one per line).”
• contaminantsstring“sequences an overrepresented read is matched against for its possible source, in FastQC's --contaminants format (a name, a tab, a sequence, one per line).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• readsstringrequired“the reads: FASTQ (quality kept in the SAM) or FASTA (QUAL written as `*`).”
• matesstring“mate-2 reads, pairing record for record with `reads`.”
• referencestring“what to map against: bases, or a FASTA with one or more records.”
• presetstring“what is being mapped (`-x`): it sets every option below to minimap2's values for that data.”
• homopolymer_compressedboolean“seed on homopolymer-compressed sequence (`-H`), so runs of one base count once: the PacBio CLR preset's answer to its length errors in homopolymers.”
• knumber“k-mer size of the minimizer seeds (`-k`).”
• wnumber“minimizer window (`-w`): one seed kept per this many consecutive k-mers.”
• max_seed_occurrencenumber“seeds occurring more often than this in the reference are skipped (`-f`); the query length they cover is what `rep_len` reports, and it lowers MAPQ.”
• min_minimizersnumber“fewest seeds a chain may have (`-n`).”
• bandwidthnumber“band of the chaining and alignment dynamic programming (`-r`, first value): the most the two sequences may drift against each other inside one chain.”
• bandwidth_longnumber“wider band for the long join (`-r`, second value): when the best chain leaves much of a long read unexplained, its seeds are re-chained in this band.”
• max_gapnumber“a chain stops at a gap longer than this between seeds (`-g`).”
• min_chain_scorenumber“lowest chaining score kept (`-m`), roughly the number of matching bases the seeds cover.”
• match_scorenumber“score per matching base (`-A`).”
• mismatch_penaltynumber“penalty per mismatch (`-B`).”
• transition_penaltynumber“penalty for a transition (A↔G, C↔T) mismatch (`-b`); 0 scores it as any mismatch.”
• gap_opennumber“gap-open penalty of the short-gap cost (`-O`, first value).”
• gap_open_longnumber“gap-open penalty of the long-gap cost (`-O`, second value); a gap costs the cheaper of the two.”
• gap_extendnumber“per-base extension of the short-gap cost (`-E`, first value).”
• gap_extend_longnumber“per-base extension of the long-gap cost (`-E`, second value).”
• zdropnumber“Z-drop (`-z`): stop extending when the score falls this far below its best, which clips a read at a junction instead of forcing it through.”
• noncanonical_penaltynumber“cost of a splice site that is not GT..AG, GC..AG or AT..AC (`-C`).”
• max_intronnumber“longest intron an alignment may span (`-G`); it also sets the reference gap and both chaining bands, as minimap2 does.”
• zdrop_inversionnumber“Z-drop at which a stalled long alignment is tested for an inversion (`-z`, second value); an inverted segment found there is written as its own record.”
• end_bonusnumber“bonus for reaching the read's end (`--end-bonus`); higher prefers end-to-end alignment over soft-clipping.”

and 54 more not listed here.

• aligned_readstringrequired“gapped read (query) row.”
• aligned_refstringrequired“gapped reference (target) row.”
• target_namestring“what to call the reference in the report row.”
• read_namestring“what to call the read in the report row.”
• target_lennumberrequired“reference length in bp.”
• verified_ungapped_pctnumber“ungapped identity required to grade a read verified — NOT the gap-inclusive `identity` output.”
• verified_coverage_pctnumber“reference coverage required to grade a read verified.”
• verified_max_gapsnumber“gaps tolerated in a verified alignment.”
• near_ungapped_pctnumber“ungapped identity required to grade a read near — NOT the gap-inclusive `identity` output.”
• near_coverage_pctnumber“reference coverage required to grade a read near.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• textstringrequired“the file's contents — a per-base coverage TSV (pos / ref / reads_all), or the provider's summary text.”
• kindstring“which report this is; `auto` sniffs it.”
• coverage_linenumber“the depth a position must reach to count as well covered.”
• step_windownumber“positions either side of a boundary whose MEDIAN depth is compared, when looking for a sudden change in level.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestring“the template to amplify — wire a record, name a library document, or leave unset to use the open record.”
• enzymestring“the Type-IIS enzyme the assembly will use.”
• left_overhangstringrequired“the top-strand overhang to leave at the START of the released part — its length must match the enzyme's own overhang.”
• right_overhangstringrequired“the top-strand overhang to leave at the END of the released part.”
• target_tmnumber“target annealing temperature for the template-binding footprint.”
• buffer_basesstring“5' buffer bases outside the recognition site, so the enzyme has somewhere to sit (NEB recommends 6 nt).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• body_mdstringrequired“the notebook entry body (markdown).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• rootobjectrequired“a history-node tree.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• seqstringrequired“the RNA/DNA sequence (T read as U).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• tablenumber“NCBI genetic-code table id (1 = standard).”
• to_stopboolean“stop at the first stop codon instead of emitting the stop symbol.”
• cdsboolean“strict CDS: require a length multiple of 3, a start codon and a terminal stop (errors otherwise).”
• featurestring“translate this annotated coding feature by NAME instead of the selection (e.g.”
• reverseboolean“read the region as the reverse complement.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• min_sizenumber“minimum ORF size.”
• alternative_startsboolean“also accept GTG/CTG as start codons (not just ATG).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• enzymesarrayrequired“enzymes to digest with — resolved against the bundled cut catalog (REBASE spellings; smaller than the REBASE dossier the editor shows).”
• fragment_indexnumber“which fragment to emit as the downstream record (0-based, in cut order).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• windownumber“sliding-window size; unset = one value for the whole sequence.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• doubleStrandedboolean“weigh BOTH strands (a plasmid or any dsDNA record) rather than the one strand written in the file (an oligo, an RNA, an alignment row).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• proteinstringrequired“the protein sequence (unambiguous one-letter codes); wire it from translate_sequence.”
• momentWindownumber“sliding window for the hydrophobic moment, in residues (default 11; clamped to the sequence length).”
• cystineConventionstring“how the oxidised e280 counts cysteines: 'cystine' = 125 per disulfide (ProtParam, default) or 'perCysteine' = 62.5 per residue (SnapGene).”
• gravyScalestring“hydropathy scale GRAVY is averaged over (all 28 ProtParam/ProtScale scales; default Kyte & Doolittle).”
• pHnumber“pH the net charge is reported at (default 7.0).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• proteinstringrequired“the protein sequence (unambiguous one-letter codes); wire it from translate_sequence.”
• kindstring“which profile to compute.”
• scalestring“hydropathy scale.”
• scaleIdstring“any of the 57 ExPASy ProtScale scales, or the 14 Biopython tables ProtScale does not publish.”
• normalizeboolean“ProtScale's 'normalize the scale from 0 to 1' — rescales the twenty scale values before windowing, so profiles from different scales are comparable.”
• windownumber“ProtScale window in residues, odd (default 9).”
• edgenumber“ProtScale relative weight of the window's edge residues, 0-1 (default 1 = unweighted).”
• weightVariationstring“ProtScale's weight model between the centre and the edge weight: 'linear' steps down evenly, 'exponential' decays steeply near the centre.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• proteinstringrequired“the protein sequence (unambiguous one-letter codes); wire it from translate_sequence.”
• kingdomstring“which of von Heijne's training sets to score against: 161 aligned eukaryotic or 36 prokaryotic signal peptides.”
• minWeightnumber“report sites scoring strictly above this.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• proteinstringrequired“the protein sequence (unambiguous one-letter codes); wire it from translate_sequence.”
• windownumber“sliding window in residues (default 11).”
• anglenumber“rotational angle per residue in degrees: 100 for an alpha-helix (default), 160 for a beta-sheet.”
• minWindowsnumber“shortest run of same-class windows reported as a segment (default 2; a one-window run is usually noise).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• proteinstringrequired“the protein sequence (unambiguous one-letter codes); wire it from translate_sequence.”
• decodingstring“which decoder: 'viterbi' the single most probable state path (default, and the fast one); 'posterior-viterbi' and 'optimal-accuracy' re-decode over the posteri…”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• proteinstringrequired“the protein sequence (unambiguous one-letter codes); wire it from translate_sequence.”
• windownumber“sliding window in residues, odd so a window has a centre residue to report at (default 51, the size the FoldIndex paper uses).”
• chargeModelstring“'net' counts whole charges K+R−D−E, which is what the paper does; 'henderson-hasselbalch' uses fractional charges at `pH`.”
• pHnumber“pH for the Henderson-Hasselbalch model, ignored by 'net' (default 7.0, the pH the paper's ⟨R⟩ is defined at).”
• pKaSetstring“named pKa set for the Henderson-Hasselbalch model (default IPC_protein, which is idpr's).”
• countHistidineboolean“count histidine as positive in the 'net' model.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• proteinstringrequired“the protein sequence; wire it from translate_sequence.”
• versionstring“which trained network: V3 (the package default), V2, or V1 (the published 2021 network).”
• thresholdnumber“smoothed score above which a residue can seed an IDR, and per-residue score at or above which it counts as disordered.”
• minimumIdrSizenumber“the shortest IDR the domain caller reports, in residues; also sets the smoothing window (twice this, made odd).”
• minimumFoldedDomainnumber“gaps between IDRs shorter than this are re-tested at 0.75× the threshold, so short ordered stretches inside an IDR are absorbed.”
• gapClosurenumber“the longest run of sub-threshold residues closed when flanked by disordered runs of the same length.”
• convertboolean“read B as N, U as C, X as G and Z as Q, as metapredict's FASTA readers do; off refuses them.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• proteinstringrequired“the protein sequence (unambiguous one-letter codes); wire it from translate_sequence.”
• enzymestring“protease or chemical (single-enzyme digest), or 'custom' to use `customCleave`.”
• enzymesarray“two or more proteases for a multi-enzyme digest; overrides `enzyme`.”
• customCleavearray“cleaving rules for the 'custom' enzyme, in RPG grammar: the comma is the cut, so '(,A)' cleaves before A and '(K or R,)' after K or R.”
• customExceptionsarray“exceptions for the 'custom' enzyme; each must repeat the rule it blocks, e.g.”
• customRegexstring“the 'custom' enzyme as a regular expression instead of RPG grammar (pyteomics' `rule=`): it matches at P1 and the cut falls after the match, e.g.”
• modestring“multi-enzyme only.”
• missedCleavagesnumber“single enzyme: allow up to this many internal sites per peptide (pyteomics).”
• keilExceptionsboolean“apply Keil's exception rules (sites trypsin does NOT cut despite matching).”
• semiboolean“also emit semi-enzymatic peptides (one ragged terminus).”
• minLengthnumber“drop peptides shorter than this (residues).”
• maxLengthnumber“drop peptides longer than this (residues).”
• massMinnumber“keep only peptides at or above this monoisotopic mass [Da]; omit for no lower bound.”
• massMaxnumber“keep only peptides at or below this monoisotopic mass [Da]; omit for no upper bound.”
• chargesarray“charge states to report m/z for, e.g.”
• cysteinestring“cysteine alkylation applied before the digest, as ExPASy PeptideMass offers it.”
• metOxidationstring“methionine oxidation.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestringrequired“peptide: one-letter residues, optionally ProForma tags on residues and termini (a signed mass, a Unimod name, or UNIMOD:accession).”
• ionTypestring“weigh the peptide as this ion; M is the intact molecule.”
• chargesarray“charge states to report m/z for (positive integers).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestringrequired“peptide: one-letter residues, optionally ProForma tags, e.g.”
• ionTypesarray“ion series to generate.”
• maxChargenumber“highest fragment charge (every charge from 1 up to it).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestringrequired“peptide, plain one-letter residues.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestring“peptide, plain one-letter residues; give this or `formula`.”
• formulastring“elemental formula of a neutral compound (C29H31N7O; isotopes as C[13]); give this or `sequence`.”
• maxIsotopenumber“peaks to keep (M counts as one); 0 keeps every peak.”
• chargenumber“protons added; masses then include them (divide by the charge for m/z).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• peptidestringrequired“candidate peptide, one-letter residues with optional ProForma tags (a signed mass, a Unimod name, or UNIMOD:accession).”
• mzarrayrequired“observed peak m/z values.”
• intensityarrayrequired“observed peak intensities, one per m/z.”
• precursorChargenumber“precursor charge; fragments are generated at charges 1 to max(1, charge - 1).”
• tolerancenumber“fragment match tolerance.”
• toleranceUnitstring“unit of the tolerance.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• textstringrequired“the MGF file's contents.”
• titlestring“return only the spectrum with this title; empty returns every spectrum.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• textstringrequired“the mzML file's contents.”
• idstring“return only the spectrum with this native id; empty returns every spectrum.”
• msLevelnumber“return only spectra at this MS level (0 returns every level).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• psmsstringrequired“the matches as a table with a header row naming spectrum, peptide, charge and score (tab- or comma-separated); peptides are ProForma.”
• databasestringrequired“the protein database searched, as FASTA; the accession is the header up to the first space.”
• scoreColumnstring“which column holds the score inference uses, when the table carries several (OpenMS score_type); a column named pep or q-value sets its own direction.”
• higherIsBetterboolean“true for scores like HyperScore; false for e-values, q-values and PEPs.”
• scoresArePepboolean“the scores are posterior error probabilities: matches compete lowest first, and each protein combines 1 − PEP into a posterior probability (higher is better); …”
• aggregationstring“how a protein's peptide scores combine: best one, mean (sum over count), or product.”
• chargeVariantsSeparateboolean“count each charge state of a peptide as its own evidence.”
• modificationVariantsSeparateboolean“count each modified form of a peptide as its own evidence.”
• useSharedPeptidesboolean“let a peptide that maps to several proteins count for each of them.”
• minPeptidesnumber“report only proteins with at least this many evidences (0 reports every matched protein).”
• greedyGroupResolutionboolean“razor peptides: give each shared peptide only to its best-scoring protein or group (ties to the one with more matches) and drop proteins left with no peptide o…”
• peptideProteinResolutionboolean“resolve shared peptides between indistinguishable groups: in each connected set of groups the highest-probability group (then the one with more peptides) takes…”
• maxAmbiguousResiduesnumber“how many ambiguous database residues (B, J, Z, X) one peptide match may resolve.”
• ilEquivalentboolean“treat isoleucine and leucine (and a database J) as the same residue when mapping peptides.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• psmsstringrequired“the matches as a table with a header row naming spectrum, peptide, charge and a posterior error probability column (tab- or comma-separated); peptides are ProF…”
• databasestringrequired“the protein database searched, as FASTA; the accession is the header up to the first space.”
• scoreColumnstring“the column holding each match's posterior error probability (PEP, 0 to 1).”
• alphanumber“peptide emission probability α: the chance a present protein yields a given one of its peptides.”
• betanumber“spurious emission probability β: the chance a peptide is reported with none of its proteins present.”
• gammanumber“protein prior γ: the chance a protein is present before any evidence.”
• peptidePriornumber“peptide prior π, dividing each match's probability back out of its evidence.”
• psmCutoffnumber“drop matches whose probability (1 − PEP) is below this.”
• gridSearchboolean“choose α, β and γ instead: run OpenMS's grid (α 0.1–0.8 × β 0.01–0.4 × γ 0.2–0.7) and keep the combination whose protein posteriors best agree with target-deco…”
• decoyPrefixstring“accession prefix marking a decoy protein, for the grid search.”
• appendReversedDecoysboolean“add the reversed sequence of every database protein as a decoy (accession decoyPrefix + accession), for a database searched with reversed decoys that holds onl…”
• maxAmbiguousResiduesnumber“how many ambiguous database residues (B, J, Z, X) one peptide match may resolve.”
• ilEquivalentboolean“treat isoleucine and leucine (and a database J) as the same residue when mapping peptides.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• scoresarrayrequired“one score per match.”
• isDecoyarrayrequired“one flag per match: true when it is a decoy hit.”
• higherIsBetterboolean“true for scores like HyperScore; false for e-values and PEPs.”
• formulanumber“1: decoys / targets.”
• rationumber“decoy-to-target database size ratio.”
• correctionnumber“0 none; 1 the +1 correction; 2 finite-sample expectation; a value in (0, 1) is a confidence level.”
• thresholdnumber“q-value cut-off for the accepted count.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• nucleasestring“the nuclease (PAM + spacer length) to scan for.”
• region_startnumber“restrict results to guides starting at/after this position (0-based).”
• region_endnumber“restrict results to guides ending at/before this position.”
• restriction_enzymesarray“cloning enzymes whose recognition site must NOT appear in the spacer.”
• min_stemnumber“minimum self-complementary stem to report.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• read_countsstringrequired“the count table: a header line, then one row per reagent — identifier, gene, then one column per sequenced sample.”
• essential_genesstringrequired“reference ESSENTIAL gene symbols, one per line (extra columns ignored).”
• non_essential_genesstringrequired“reference NON-ESSENTIAL gene symbols, one per line.”
• control_columnsarrayrequired“the T0 / plasmid column NAMES, exactly as the header spells them.”
• sample_columnsarray“which sample column names to score.”
• min_readsnumber“drop a reagent whose SUMMED control count is below this (upstream's -m).”
• pseudo_countnumber“added to every count before normalising to 10,000,000 reads per column.”
• equalise_replicatesnumber“scale every Bayes factor as if the screen had this many replicates (upstream's -p), 0 to leave it off.”
• fdr_cutnumber“the false-discovery rate the hit list is cut at.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• spacersarrayrequired“the protospacers to screen (20 nt for SpCas9) — wire `topSpacer` or the spacers out of a design run, or list them.”
• backbonestring“which sgRNA backbone the spacer will be cloned into — the hairpin test is against this.”
• ggboolean“the construct starts the transcript GG — upstream's `-gg` REPLACES the spacer's first two bases with G (T7 preference), it does not lengthen it.”
• pre_gboolean“the construct prepends a single 5' G (upstream's `-preG`) — this one lengthens the scanned string, and upstream's fixed 17-window loop then never reaches its l…”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• spacerstringrequired“the protospacer to search for (20 nt for SpCas9).”
• subjectstring“the sequence to search — wire a record or name a library document; leave unset to search the open record.”
• nucleasestring“which nuclease's PAM and geometry to use.”
• max_mismatchesnumber“how many mismatches a site may carry and still be reported.”
• limitnumber“cap the rows returned (hits come back worst-first: fewest mismatches).”
• dna_bulgenumber“extra bases in the DNA a site may carry (a gap opened in the guide).”
• rna_bulgenumber“extra bases in the guide a site may carry (a gap opened in the DNA).”
• circularboolean“search across the origin as well.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• spacersarrayrequired“the protospacers to count — wire the spacers out of a design run, or list them.”
• subjectstring“the sequence to search — wire a record or name a library document; leave unset to search the open record.”
• nucleasestring“which nuclease's PAM and geometry to use.”
• max_mismatchesnumber“how many mismatches a site may carry and still be counted.”
• dna_bulgenumber“extra bases in the DNA a site may carry.”
• rna_bulgenumber“extra bases in the guide a site may carry.”
• circularboolean“count across the origin as well.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• spacerstringrequired“the protospacer to fold.”
• nucleasestring“picks the scaffold published for that nuclease.”
• sg_rnaboolean“also fold the full spacer+scaffold sgRNA, not just the spacer.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestring“the DNA to scan - leave unset to use the open record.”
• strandstring“which strand to read.”
• min_maxentnumber“report only sites at or above this MaxEntScan score, in bits.”
• max_resultsnumber“how many to return, strongest first.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestring“the DNA to scan - leave unset to use the open record.”
• motifsarrayrequired“the matrices, each {name, counts: {A, C, G, T} per position, relativeThreshold (0-1 of the matrix's score range) or threshold (absolute log-odds)}.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestring“the DNA to scan - leave unset to use the open record.”
• region_startnumber“0-based inclusive start of the region to scan.”
• region_endnumber“0-based inclusive end.”
• both_strandsboolean“scan the reverse strand too.”
• max_dgnumber“report only configurations at or below this ΔG_total.”
• max_resultsnumber“how many to return, strongest (most negative) first.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestring“the DNA to scan - leave unset to use the open record.”
• region_startnumber“0-based inclusive start of the region to scan.”
• region_endnumber“0-based inclusive end.”
• both_strandsboolean“scan the reverse strand too.”
• max_resultsnumber“how many to return, best hairpin first.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• mrnastring“the mRNA (or DNA) carrying the UTR and the CDS — leave unset to use the open record.”
• start_posnumberrequired“0-based position of the start codon's first base within `mrna`.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• organismstring“reference organism for CAI weights + rare codons.”
• reverseboolean“read the region as the reverse complement.”
• featurestring“score this annotated CDS or gene by NAME instead of the selection (the panel's "A CDS / feature…" mode).”
• tablestring“score CAI and rare codons against a codon-usage table this project holds, BY NAME, as the Codon Usage panel lists it — any organism, not just the two pydna cur…”
• rare_thresholdnumber“a codon is rare when its relative adaptiveness w = f/f_max falls below this.”
• enc_bg_correctionboolean“correct ENC for the sequence's own base composition (Novembre 2002).”
• enc_pairsboolean“count codon PAIRS rather than single codons for ENC (k-mer 2) — bias in the junctions rather than in the codons.”
• rcbs_directionalboolean“RCBS weights taken as max(observed/expected, expected/observed), so under-use counts as bias too rather than only over-use.”
• rcbs_meanstring“how the per-codon RCBS weights are averaged.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• synonymousboolean“normalise each amino acid's codons to sum to 1 (synCUFS), so what remains is the synonymous choice alone.”
• reverseboolean“read the region as the reverse complement.”
• featurestring“score this annotated CDS or gene by NAME instead of the selection (the panel's "A CDS / feature…" mode).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestring“the sequence to judge — defaults to the open record.”
• preserve_protein_ofstring“the ORIGINAL coding sequence (or its protein): the result must still translate to it.”
• forbid_sitesarray“enzyme names that must not cut, e.g.”
• require_frameboolean“length divisible by 3 and no premature stop.”
• require_startboolean“with require_frame: the first codon must be a start codon.”
• require_stopboolean“with require_frame: the last codon must be a stop.”
• min_lengthnumber“minimum length [bp].”
• max_lengthnumber“maximum length [bp].”
• min_gcnumber“minimum GC fraction (0-1).”
• max_gcnumber“maximum GC fraction (0-1).”
• gc_windownumber“judge every window of this many bases instead of the whole sequence — a synthesis is rejected on a local GC peak, not on the mean.”
• cai_organismstring“host for the codon-adaptation check, e.g.”
• min_cainumber“minimum CAI (needs cai_organism).”
• tablenumber“NCBI translation table.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• constraintsarray“DnaChisel constraint specs, e.g.”
• objectivesarray“DnaChisel objective specs — soft goals the solver maximises.”
• candidatesnumber“how many alternative solutions to produce (1 = a single solve).”
• seednumber“base seed for the alternatives — the same seed returns the same set.”
• randomization_thresholdnumber“DnaChisel `randomization_threshold` (default 10000).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• cdsstring“the CDS starting at its start codon; unset = the open record's sequence.”
• target_strengthnumberrequired“target relative strength, on the model's own scale — 1 is as strong as its reference site, and real sites do score above it.”
• upstreamstring“upstream context 5' of the UTR (engine default when unset).”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• region_startnumber“0-based inclusive start of the region to design into (LAMP designs into a stretch, not a whole plasmid).”
• region_endnumber“0-based inclusive end.”
• max_setsnumber“how many sets to return, best first.”
• loop_primersboolean“design LF/LB as well.”
• end_stability_dgnumber“the terminal-6-base stability rule (manual §2.2: the ΔG "is -4 kcal/mol or less").”
• end_stability_ntnumber“how many terminal bases the end-stability rule measures (manual §2.2: 6).”
• length_minnumber“length window for the outer/inner binding regions (manual §4.2) - lower bound.”
• length_maxnumber“length window for the outer/inner binding regions (manual §4.2) - upper bound.”
• tm_inner_minnumber“Tm window for F1c / B1c - the manual's "about 65 °C" - lower bound.”
• tm_inner_maxnumber“Tm window for F1c / B1c - the manual's "about 65 °C" - upper bound.”
• tm_outer_minnumber“Tm window for F2 / B2 / F3 / B3 - the manual's "about 60 °C" - lower bound.”
• tm_outer_maxnumber“Tm window for F2 / B2 / F3 / B3 - the manual's "about 60 °C" - upper bound.”
• tm_loop_minnumber“Tm window for the loop primers LF / LB - lower bound.”
• tm_loop_maxnumber“Tm window for the loop primers LF / LB - upper bound.”
• gc_minnumber“GC FRACTION window, 0-1 (manual §2.3: "between about 40% to 65%") - lower bound.”
• gc_maxnumber“GC FRACTION window, 0-1 (manual §2.3: "between about 40% to 65%") - upper bound.”
• amplified_span_minnumber“F2 5' to B2 5', the amplified region.”
• amplified_span_maxnumber“F2 5' to B2 5', the amplified region.”
• loop_span_minnumber“5' of F2 to 5' of F1 - the portion that forms the loop (manual §2.5: 40-60) - lower bound.”
• loop_span_maxnumber“5' of F2 to 5' of F1 - the portion that forms the loop (manual §2.5: 40-60) - upper bound.”
• outer_gap_minnumber“F3 to F2 and B3 to B2 gap.”
• outer_gap_maxnumber“F3 to F2 and B3 to B2 gap.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• alignmentarray“the ALIGNED PROTEIN rows, each { name, sequence } in one-letter amino acids with gaps preserved - wire an upstream protein alignment here.”
• alignment_fastastring“an aligned PROTEIN FASTA, when there is no upstream alignment to wire.”
• tablestringrequired“the codon-usage table to back-translate the clamp through, BY NAME as the Codon Usage panel lists it.”
• block_indexnumber“which gapless block to design in, 0-based, ordered as `gaplessBlocks` returns them (blocks of at least 8 ungapped columns).”
• strandstring“which strand to design on.”
• max_core_degeneracynumber“degeneracy ceiling for the 3' core (Rose 2003 step 7: "a maximum degeneracy of 128").”
• clamp_tmnumber“target melting temperature for the non-degenerate 5' clamp (Rose 2003 step 8: "the current default is 60 °C, which usually provides a clamp of ~20 nucleotides"…”
• conditionsobject“salt, magnesium, dNTP and oligo concentrations plus the salt-correction method and any additives the clamp Tm is measured in.”
• max_runnumber“longest single-base run allowed; 2003's stated polynucleotide run limit.”
• base_cutoffnumber“minimum predicted probability for a base to enter the degenerate core.”
• max_clamp_lengthnumber“ceiling on clamp growth, so an unreachable Tm REFUSES instead of consuming the whole block.”
• genetic_code_idnumber“NCBI `transl_table` id for the codon-to-residue map.”
• core_lengthsarray“core lengths the scan tries, in residues — every length here is scanned and the best-scoring core kept.”
• weightingstring“how the alignment's rows are weighted before the core's consensus is read.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• alignmentarray“the ALIGNED rows to scan, each `{ name, sequence }` with gaps preserved - wire an upstream `align_sequences` rows output here.”
• alignment_fastastring“an aligned FASTA to scan, when there is no upstream alignment to wire.”
• algorithmstring“which search picks each window's oligo.”
• lengthnumber“oligomer length (DegePrime `-l`).”
• max_degeneracynumber“degeneracy ceiling (`-d`) - how many distinct oligos the IUPAC code is allowed to stand for.”
• min_productnumber“shortest product, in TRIMMED alignment columns.”
• max_productnumber“longest product, in TRIMMED alignment columns.”
• min_fraction_matchingnumber“a window must bind at least this fraction of the spanning sequences to be a candidate - the coverage floor, and the number that decides whether 'every homologu…”
• trim_cutoffnumber“columns occupied by less than this fraction of sequences are dropped before scanning.”
• min_depthnumber“fewest gapless sequences a window needs before it is reported at all (`-depth`).”
• skipnumber“bases excluded at each end of every sequence (`-skip`).”
• iterationsnumber“WRM restarts (`-iter`).”
• seednumber“seed for WRM's draw, so a run is REPRODUCIBLE.”
• exhaustive_mer_limitnumber“largest number of distinct mers `exhaustive` will attempt before refusing a window.”
• limitnumber“how many pairs to return, best coverage first.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• assaystring“BSP = bisulfite sequencing PCR: primers avoid CpG sites so both methylated and unmethylated template amplify equally, and the methylation is read from the SEQU…”
• max_resultsnumber“how many primer pairs to return, best first.”
• region_startnumber“0-based inclusive start of the region to design in.”
• region_endnumber“0-based inclusive end.”
• criteriastring“which published criteria call a CpG island: Gardiner-Garden & Frommer 1987 as EMBOSS cpgplot encodes it, or the stricter Takai & Jones 2002, which excludes mos…”
• island_windownumber“sliding window over which C, G and CpG are counted (cpgplot -window); unset takes the preset's.”
• island_min_lengthnumber“minimum island length (cpgplot -minlen); unset takes the preset's.”
• island_min_obs_expnumber“minimum observed/expected CpG (cpgplot -minoe); unset takes the preset's.”
• island_min_percentnumber“minimum %C+%G (cpgplot -minpc); unset takes the preset's.”
• design_in_islandnumber“design inside this island only, by its rank in the reported list (1 = first).”
• min_lengthnumber“shortest primer considered.”
• opt_lengthnumber“primer length the ranking prefers.”
• max_lengthnumber“longest primer considered.”
• min_tmnumber“primers below this Tm are rejected outright.”
• opt_tmnumber“target Tm; candidates rank by distance from it.”
• max_tmnumber“primers above this Tm are rejected outright.”
• min_gcnumber“lowest acceptable GC.”
• max_gcnumber“highest acceptable GC.”
• product_minnumber“shortest acceptable amplicon.”
• product_maxnumber“longest acceptable amplicon.”
• min_non_cpg_cnumber“BSP ONLY.”
• min_cpgnumber“MSP ONLY.”
• max_cpg_distance_from_3number“MSP ONLY.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• read_lengthnumber“usable bases per read, AFTER the dead zone.”
• dead_zonenumber“bases at the start of a read that are not trustworthy.”
• overlapnumber“confirmed overlap required between consecutive reads on one strand.”
• both_strandsboolean“read every base from both directions - what a sequencing facility means by double-stranded coverage, and the standard for anything deposited or published.”
• region_startnumber“0-based inclusive start of the region to read.”
• region_endnumber“0-based inclusive end of the region to read.”
• target_tmnumber“target melting temperature for each primer in the walk.”
• min_lengthnumber“shortest acceptable primer.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• target_tmnumber“target melting temperature (pydna default 55).”
• conditionsobject“salt, magnesium, dNTP and oligo concentrations plus the salt-correction method and any additives the target Tm is measured in.”
• limitnumber“minimum primer length (pydna `limit`).”
• forward_primerstring“supply one primer to design only its mate.”
• reverse_primerstring“supply one primer to design only its mate.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencesarray“the sequences to align — wire several upstream outputs here, or list library document names/ids.”
• include_subjectboolean“also align the node's subject (the open or wired record).”
• enginestring“which aligner builds the alignment.”
• global_alignboolean“global alignment rather than local.”
• matchnumber“`poa` only: score for a pair of identical symbols.”
• mismatchnumber“`poa` only: score for a mismatching pair.”
• gapnumber“`poa` only: score for a gap column.”
• align_matrixstring“`progressive` only: the substitution matrix the ALIGNMENT itself is scored with - distinct from `score_matrix`, which only scores the quality report afterwards.”
• guide_treestring“`progressive` only: which tree the merge follows.”
• affine_gapboolean“`progressive` only: `false` charges one flat penalty per gap column; `true` charges separate opening and extension penalties, which is what keeps a real indel …”
• gap_penaltynumber“`progressive` only: the flat penalty per gap column.”
• gap_opennumber“`progressive`, affine only: the penalty for STARTING a gap.”
• gap_extendnumber“`progressive`, affine only: the penalty for each column a gap is extended by.”
• terminal_penaltyboolean“`progressive` only: `true` charges overhanging ends like an internal gap - right for full-length homologues.”
• score_matrixstring“substitution matrix for the pyMSA sum-of-pairs and star scores in the quality report.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• rowsarrayrequired“the ALIGNED rows, each {name, aligned}; every row must already be the same length.”
• fromnumber“first column drawn, 1-based and inclusive.”
• columnsnumber“how many columns to draw.”
• schemestring“identity shades a residue by how much of its column agrees with it, which works for any alphabet; nucleotide paints QUEEN's own base colours and is IGNORED ove…”
• cell_widthnumber“width of one column's cell.”
• row_heightnumber“height of one row.”
• name_charsnumber“how many characters of a row's name to print; a longer one is elided in the middle, keeping the tail where two rows of a family differ.”
• conservationboolean“print the conservation line under the block.”
• rulerboolean“print the column numbers over the block.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• textstringrequired“the alignment file's contents.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• fragmentsarray“the fragments to assemble — wire upstream `record` outputs here, or list library document names/ids.”
• include_subjectboolean“also include the node's subject as a fragment.”
• min_homology_bpnumber“minimum terminal homology for two ends to join.”
• max_homology_bpnumber“longest terminal homology considered.”
• min_tmnumber“optional floor on the junction's GATE value (DnaCauldron's naive A/T = 2, G/C = 4 sum, not a nearest-neighbour temperature).”
• max_tmnumber“optional ceiling on the same gate scale.”
• topologystring“product topology to enumerate.”
• preserve_backbone_originboolean“for circular products, rotate the origin to the start of the backbone fragment and name the product after it.”
• expect_no_unused_partsboolean“treat a fragment left out of every construct as an error rather than a warning (upstream's own default).”
• max_constructsnumber“cap on how many distinct constructs are enumerated, so an ambiguous fragment set cannot run away.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• fragmentsarray“the fragments to join, IN ASSEMBLY ORDER — wire upstream `record` outputs here, or list library document names/ids.”
• include_subjectboolean“put the node's subject first, as the backbone.”
• target_tmnumber“target annealing Tm for each primer's 3' footprint.”
• overlapnumber“homology shared between two adjacent fragments.”
• circularboolean“close the ring: the last fragment also overlaps the first.”
• min_footprintnumber“shortest annealing footprint the designer may settle for (pydna's `limit`).”
• synthesis_scalestring“catalogue product to price the oligos at (an `oligo-list-prices` record id); `auto` prices each at the cheapest product whose published length range covers it.”
• conditionsobject“salt, magnesium, dNTP and oligo concentrations plus the salt-correction method the target Tm is measured in.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• partsarray“the parts to assemble — wire upstream `record` outputs here, or list library document names/ids.”
• include_subjectboolean“also include the node's subject as a part.”
• enzymestring“Type-IIS enzyme, or leave unset to let DnaCauldron pick one.”
• connectorsarray“candidate bridging LINKERS, a library distinct from `parts`.”
• expected_constructsnumber“expect exactly this many constructs and fail when the count differs.”
• expect_no_unused_partsboolean“treat a part the assembly did not consume as an error, which is DnaCauldron's own default.”
• max_constructsnumber“cap on enumerated constructs.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• partsarray“the parts to check — wire upstream `record` outputs here, or list library document names/ids.”
• include_subjectboolean“also check the node's subject.”
• enzymestring“the Type-IIS enzyme the assembly will use.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• overhangsarrayrequired“the junction overhangs, one per junction, top strand (e.g.”
• enzymestring“the Type-IIS enzyme the reaction uses, which picks that enzyme's own measured matrix when one exists.”
• datasetstring“score against this measured matrix instead of the one the enzyme implies.”
• remediesboolean“also compute what to CHANGE: the drop-the-worst repair, and replacement candidates for each flagged junction.”
• replacements_per_junctionnumber“how many replacement candidates to rank per flagged junction.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sequencestring“the sequence to fragment, in one piece.”
• min_lengthnumber“shortest allowed fragment, in bases — usually what your synthesis vendor will accept.”
• max_lengthnumber“longest allowed fragment, in bases — the vendor's upper limit, or the length you can sequence in one read.”
• tracesnumber“how many ranked alternatives to return.”
• fragmentsnumber“pin the number of fragments instead of letting the search choose.”
• efficiency_weightnumber“exponent on the running ligation EFFICIENCY — raise it to favour junctions that ligate readily.”
• fidelity_weightnumber“exponent on the running FIDELITY — raise it to favour junctions that ligate to the right partner rather than a mismatched one.”
• max_overhang_identitynumber“most positions two overhangs in the set may share before they are treated as confusable.”
• alien_overhangsarray“junctions already committed elsewhere in the assembly (a fixed vector's own ends), which this set must not collide with.”
• exclude_fromnumber“start of a span no cut may fall in — a feature you need kept intact.”
• exclude_tonumber“end of that span, exclusive.”
• datasetstring“the measured ligation matrix to score against.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• sizenumber“how many junctions the assembly needs (parts + 1 for a circular construct, counted as junctions).”
• fixedarray“junctions you cannot change, such as a destination vector's own overhangs.”
• enzymestring“the Type-IIS enzyme the reaction uses, which picks that enzyme's own measured matrix when one exists.”
• datasetstring“design against this measured matrix instead of the one the enzyme implies.”
• start_fromarray“the set you already have, as a second starting point.”
• candidate_poolnumber“how many of the strongest-annealing overhangs the search considers.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• partsarray“the physical parts — wire upstream `record` outputs here, or list library document names/ids.”
• planstringrequired“the plan, in DnaCauldron's spreadsheet shape: one line per construct, `name,partA,partB`.”
• methodstring“the assembly chemistry every step uses (upstream passes one class per spreadsheet).”
• include_subjectboolean“also offer the node's subject as a part.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”

• min_tempnumber“lowest temperature to evaluate.”
• max_tempnumber“highest temperature to evaluate.”
• stepnumber“grid spacing; finer costs proportionally more.”
• region_startnumber“0-based inclusive start of the region to melt.”
• region_endnumber“0-based inclusive end.”
• ionsnumber“molar sodium-equivalent concentration.”
• _subjectobject“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 pic…”
• _filesarray“The project: record references shaped like _subject.”