workbench

Previous value: -"1-based CONTROL position of the intended edit. Give it when you know it: without it the most-edited significant position is labelled the target and the rest become bystanders, which relabels a bystander-dominant result as a clean one."New value: +"1-based CONTROL position of the intended edit. Give it when you know it: without it the most-edited significant position is labeled the target and the rest become bystanders, which relabels a bystander-dominant result as a clean one."

Previous value: -"Annealing temperature actually used, °C. Compared against each primer's own nearest-neighbour Tm."New value: +"Annealing temperature actually used, °C. Compared against each primer's own nearest-neighbor Tm."

Previous value: -"The Type IIS enzyme for Golden Gate (BsaI, BbsI, Esp3I (BsmBI)), or the one or two restriction enzymes the insert and vector were cut with. An unrecognised name is rejected rather than skipped: every methylation and site-geometry verdict here reads \"no site found\" when the enzyme is missing, so a typo would come back as a clean bill of health."New value: +"The Type IIS enzyme for Golden Gate (BsaI, BbsI, Esp3I (BsmBI)), or the one or two restriction enzymes the insert and vector were cut with. An unrecognized name is rejected rather than skipped: every methylation and site-geometry verdict here reads \"no site found\" when the enzyme is missing, so a typo would come back as a clean bill of health."

Previous value: -"Annealing temperature actually used, °C. Compared against each primer's own nearest-neighbour Tm."New value: +"Annealing temperature actually used, °C. Compared against each primer's own nearest-neighbor Tm."

Previous value: -"The Type IIS enzyme for Golden Gate (BsaI, BbsI, Esp3I (BsmBI)), or the one or two restriction enzymes the insert and vector were cut with. An unrecognised name is rejected rather than skipped: every methylation and site-geometry verdict here reads \"no site found\" when the enzyme is missing, so a typo would come back as a clean bill of health."New value: +"The Type IIS enzyme for Golden Gate (BsaI, BbsI, Esp3I (BsmBI)), or the one or two restriction enzymes the insert and vector were cut with. An unrecognized name is rejected rather than skipped: every methylation and site-geometry verdict here reads \"no site found\" when the enzyme is missing, so a typo would come back as a clean bill of health."

Previous value: -"Vector sequence (restriction, topo and lic methods; for lic, the LINEARISED vector)."New value: +"Vector sequence (restriction, topo and lic methods; for lic, the LINEARIZED vector)."

Previous value: -"Protein sequence (one-letter codes). Coding DNA/RNA is accepted and translated in frame +1 up to the first stop codon (residues after an in-frame stop are NOT optimised)."New value: +"Protein sequence (one-letter codes). Coding DNA/RNA is accepted and translated in frame +1 up to the first stop codon (residues after an in-frame stop are NOT optimized)."

Previous value: -"Enzyme names whose internal sites should be flagged as errors. Matched against the curated common-enzyme set plus the Golden Gate Type IIS enzymes (BsaI, BbsI, Esp3I/BsmBI); an unrecognised name is rejected, never skipped."New value: +"Enzyme names whose internal sites should be flagged as errors. Matched against the curated common-enzyme set plus the Golden Gate Type IIS enzymes (BsaI, BbsI, Esp3I/BsmBI); an unrecognized name is rejected, never skipped."

Previous value: -"Restrict the search to these enzymes (e.g. the ones on your bench). Default is the whole curated set of 49. An unrecognised name is rejected rather than skipped, so \"does not discriminate\" always means it was actually tried."New value: +"Restrict the search to these enzymes (e.g. the ones on your bench). Default is the whole curated set of 49. An unrecognized name is rejected rather than skipped, so \"does not discriminate\" always means it was actually tried."

Previous value: -"Per-base [A, C, G, T] intensities of the control read, one row per called base, read at that base's peak location (trace arrays are indexed by scan, not by base). Raw peak heights: every intensity must be >= 0, because negatives are clamped to zero during normalisation and a baseline-subtracted trace would silently lose its minor peaks and read as unedited."New value: +"Per-base [A, C, G, T] intensities of the control read, one row per called base, read at that base's peak location (trace arrays are indexed by scan, not by base). Raw peak heights: every intensity must be >= 0, because negatives are clamped to zero during normalization and a baseline-subtracted trace would silently lose its minor peaks and read as unedited."

Previous value: -"Which real ligation dataset to optimise against."New value: +"Which real ligation dataset to optimize against."

Previous value: -"Engineer the internal ARMS destabilising mismatch near the 3' end."New value: +"Engineer the internal ARMS destabilizing mismatch near the 3' end."

Previous value: -"Second oligo. Omit to analyse hairpin structure in 'a' alone; pass the same sequence as 'a' for a homodimer."New value: +"Second oligo. Omit to analyze hairpin structure in 'a' alone; pass the same sequence as 'a' for a homodimer."

Previous value: -"\"global\" penalises end gaps in both sequences; \"local\" returns the best-scoring subalignment; \"semiglobal\" is a fitting alignment — seqB is consumed end to end while seqA's terminal overhangs are free and are not emitted, so a partial read placed on a longer reference is not smeared across it."New value: +"\"global\" penalizes end gaps in both sequences; \"local\" returns the best-scoring subalignment; \"semiglobal\" is a fitting alignment — seqB is consumed end to end while seqA's terminal overhangs are free and are not emitted, so a partial read placed on a longer reference is not smeared across it."

Previous value: -"Distinct reads that must agree on the same breakpoint before a structural variant (large deletion, duplication, inversion, insertion) is reported. Default 3 — stricter than minSupportingReads on purpose: a single split read is a library-prep chimera or a mapping artefact far more often than it is biology, and chimeras are common enough that two agreeing by chance is likelier than two matching base errors."New value: +"Distinct reads that must agree on the same breakpoint before a structural variant (large deletion, duplication, inversion, insertion) is reported. Default 3 — stricter than minSupportingReads on purpose: a single split read is a library-prep chimera or a mapping artifact far more often than it is biology, and chimeras are common enough that two agreeing by chance is likelier than two matching base errors."

Previous value: -"Read type, which selects minimap2's alignment preset. \"auto\" (the default) passes no preset and uses minimap2's own defaults — whose parameters happen to be map-ont's, so nanopore data is already handled; setting \"nanopore\" makes that explicit and pins it. \"pacbio\" uses map-hifi and \"illumina\" uses sr, both of which materially change the result: under the ONT defaults gaps are cheap, so on accurate reads a cluster of mismatches can be reported as a spurious indel. \"sanger\" uses map-hifi with the minimum alignment score returned to 80, because map-hifi's own floor of 200 was chosen for 10-25 kb reads and would leave a short or partly-failed Sanger read unmapped. The preset actually used is reported back as minimap2Preset/alignerArgs so a run can be reproduced. Names are matched ignoring case and punctuation, and the obvious aliases resolve (\"ONT\" and \"map-ont\" to nanopore, \"HiFi\" to pacbio, \"sr\" to illumina); anything unrecognised is rejected rather than silently treated as \"auto\"."New value: +"Read type, which selects minimap2's alignment preset. \"auto\" (the default) passes no preset and uses minimap2's own defaults — whose parameters happen to be map-ont's, so nanopore data is already handled; setting \"nanopore\" makes that explicit and pins it. \"pacbio\" uses map-hifi and \"illumina\" uses sr, both of which materially change the result: under the ONT defaults gaps are cheap, so on accurate reads a cluster of mismatches can be reported as a spurious indel. \"sanger\" uses map-hifi with the minimum alignment score returned to 80, because map-hifi's own floor of 200 was chosen for 10-25 kb reads and would leave a short or partly-failed Sanger read unmapped. The preset actually used is reported back as minimap2Preset/alignerArgs so a run can be reproduced. Names are matched ignoring case and punctuation, and the obvious aliases resolve (\"ONT\" and \"map-ont\" to nanopore, \"HiFi\" to pacbio, \"sr\" to illumina); anything unrecognized is rejected rather than silently treated as \"auto\"."

Previous value: -"Engineer the ARMS destabilising mismatch 3 nt from the allele-specific primer's 3' end."New value: +"Engineer the ARMS destabilizing mismatch 3 nt from the allele-specific primer's 3' end."

Previous value: -"The linearised vector was CIP/rSAP-dephosphorylated (restriction method). Affects the self-ligation background warnings, not the product."New value: +"The linearized vector was CIP/rSAP-dephosphorylated (restriction method). Affects the self-ligation background warnings, not the product."

Previous value: -"Vector sequence (restriction and lic methods; for lic, the LINEARISED vector). Omit if vectorPcr is given."New value: +"Vector sequence (restriction and lic methods; for lic, the LINEARIZED vector). Omit if vectorPcr is given."

Previous value: -"Enzyme names to digest with, from the curated common-enzyme set (see restriction_sites for the full list). An unrecognised name is rejected rather than skipped, so an empty band pattern always means \"no sites\"."New value: +"Enzyme names to digest with, from the curated common-enzyme set (see restriction_sites for the full list). An unrecognized name is rejected rather than skipped, so an empty band pattern always means \"no sites\"."

Added value: +20

Added value: +1

Previous value: -"The ids to map, up to 20000 (e.g. gene symbols, UniProt accessions, Ensembl gene IDs, Entrez GeneIDs, or RefSeq protein accessions, depending on \"from\")."New value: +"The ids to map, up to 100000 (e.g. gene symbols, UniProt accessions, Ensembl gene IDs, Entrez GeneIDs, or RefSeq protein accessions, depending on \"from\")."

Previous value: -"The ids to map, up to 1000 (e.g. gene symbols, UniProt accessions, Ensembl gene IDs, Entrez GeneIDs, or RefSeq protein accessions, depending on \"from\")."New value: +"The ids to map, up to 20000 (e.g. gene symbols, UniProt accessions, Ensembl gene IDs, Entrez GeneIDs, or RefSeq protein accessions, depending on \"from\")."

Previous value: -"Nucleotide sequence (raw or FASTA). A, C, G, T, N only — other IUPAC codes are rejected rather than silently dropped, because pLannotate's search engines discard them and every coordinate after would shift. Max 30,000 bp."New value: +"Nucleotide sequence (raw or FASTA). A, C, G, T, N only — other IUPAC codes are rejected rather than silently dropped, because pLannotate's search engines discard them and every coordinate after would shift. Max 150,000 bp."

Previous value: -"Coding sequence, raw or FASTA, starting at its start codon. Only the 5' end affects the prediction, so the first ~90 nt is enough. A, C, G, T/U only. Max 3,000 nt."New value: +"Coding sequence, raw or FASTA, starting at its start codon. Only the 5' end affects the prediction, so the first ~90 nt is enough. A, C, G, T/U only. Max 10,000 nt."

Previous value: -"mRNA sequence, raw or FASTA — the 5' UTR plus at least the start of the CDS. DNA (T) and RNA (U) are both accepted and scored identically. A, C, G, T/U only. Max 3,000 nt."New value: +"mRNA sequence, raw or FASTA — the 5' UTR plus at least the start of the CDS. DNA (T) and RNA (U) are both accepted and scored identically. A, C, G, T/U only. Max 10,000 nt."

Previous value: -"Output format. fasta-cds / fasta-protein extract CDS features (GenBank input only). GenBank in and 'genbank' out rewrites the record with its features, qualifiers and topology intact — it is a rewrite, not a re-annotation."New value: +"Output format. fasta-cds / fasta-protein extract CDS features (GenBank input only). GenBank in and 'genbank' out rewrites the record with its features, qualifiers and topology intact — it is a rewrite, not a re-annotation. 'snapgene' writes a binary SnapGene .dna file, returned base64 in `fileBase64` rather than in `output`; it takes ONE record, because a .dna holds one molecule."

Previous value: -[
-  "fasta",
-  "fasta-cds",
-  "fasta-protein",
-  "genbank",
-  "tsv"
-]New value: +[
+  "fasta",
+  "fasta-cds",
+  "fasta-protein",
+  "genbank",
+  "tsv",
+  "snapgene"
+]

Added value: +{
+  "description": "Regions no primer may overlap, 1-based inclusive, as {start,end}. start > end is a region crossing the origin of a circular template.",
+  "items": {
+    "properties": {
+      "end": {
+        "type": "integer"
+      },
+      "start": {
+        "type": "integer"
+      }
+    },
+    "required": [
+      "start",
+      "end"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}

Added value: +{
+  "description": "Consecutive G/C required at the very 3' end (Primer3's PRIMER_GC_CLAMP). Omitted or 0 means no requirement.",
+  "type": "integer"
+}

Added value: +{
+  "description": "Longest run of one base a primer may contain (Primer3's PRIMER_MAX_POLY_X). Omitted or 0 means no limit.",
+  "type": "integer"
+}

Added value: +{
+  "description": "Floor on the NN ΔG37 (kcal/mol) of the five 3'-most bases; a more stable end than this is rejected. Deliberately not Primer3's max_end_stability, which is a different scale this model has not been calibrated against.",
+  "type": "number"
+}

Previous value: -"The claimed/expected reference sequence."New value: +"The claimed/expected reference — bare bases, FASTA, or a whole GenBank record. Pass the GenBank record (your own map) to get consequences: every consensus edit is then placed against the features, so the answer reads \"silent in AmpR\" or \"premature STOP at codon 41 of your CDS\" instead of only a position and a base. Bare bases still work and simply return no consequences."

Previous value: -"An rsID (\"rs1042522\"), chrom:pos:ref:alt (\"17:7676154:G:C\", single-base substitutions only), genomic HGVS (\"chr17:g.7676154G>C\" or \"17:g.7676154G>C\"), or transcript HGVS c. (\"NM_000546.6:c.215C>G\" or \"TP53:c.215C>G\")."New value: +"An rsID (\"rs1042522\"), chrom:pos:ref:alt with either separator (\"17:7676154:G:C\" or \"17-7676154-G-C\", single-base substitutions only), genomic HGVS (\"chr17:g.7676154G>C\" or \"17:g.7676154G>C\"), or transcript HGVS c. (\"NM_000546.6:c.215C>G\" or \"TP53:c.215C>G\")."

Added value: +{
+  "default": 100,
+  "description": "How many ORFs to return, longest first. `count` always reports every ORF found and `truncated` says whether the list was cut.",
+  "maximum": 5000,
+  "minimum": 1,
+  "type": "integer"
+}

Added value: +{
+  "default": 500,
+  "description": "How many matches to return. `count` always reports every hit found and `truncated` says whether the list was cut.",
+  "maximum": 20000,
+  "minimum": 1,
+  "type": "integer"
+}

Added value: +1

Added value: +{
+  "default": false,
+  "description": "Treat claimedConstruct as a circular plasmid, so an insert that spans its arbitrary numbering origin is found whole. Without it the insert is looked for linearly and a wrapped one covers only its longer half.",
+  "type": "boolean"
+}

Previous value: -"Total gapmer length (nt)."New value: +"Total gapmer length (nt). A real RNase H1 gapmer is 12-25."

Added value: +50

Added value: +8

Previous value: -"Modified-wing length on each side (nt); the central gap = length − 2×wing."New value: +"Modified-wing length on each side (nt); the central gap = length − 2×wing, so 2×wing must be less than length."

Added value: +0

Added value: +10

Added value: +1

Previous value: -"FASTQ Phred ASCII offset (33 = Sanger/Illumina 1.8+, 64 = Illumina 1.3-1.7)."New value: +"ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina."

Previous value: -"FASTQ Phred ASCII offset (33 = Sanger/Illumina 1.8+, 64 = Illumina 1.3-1.7)."New value: +"ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina."

Previous value: -"FASTQ Phred ASCII offset (33 = Sanger/Illumina 1.8+, 64 = Illumina 1.3–1.7)."New value: +"ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina."

Previous value: -"pH step for the net-charge titration curve (0–14)."New value: +"pH step along the net-charge titration curve, which always spans pH 0-14. Between 0.001 and 14."

Added value: +14

Added value: +0.001

Added value: +{
+  "default": false,
+  "description": "Include the four raw dye-channel arrays and peakLocations. They are 93% of the response — a 900-base read is 122 kB with them and 8 kB without (measured) — and they are only useful for DRAWING the chromatogram. Everything you would reason about (base calls, quality, the run's labels) is returned either way, so leave this off unless you are rendering.",
+  "type": "boolean"
+}

Added value: +{
+  "description": "Optional: the concentration you need. Supplying it (with volumeUl, so there is a stock concentration to dilute FROM) returns a `dilution` plan — µL of stock and µL of diluent — instead of leaving C1V1 = C2V2 to be done by hand. The stock and the target may be quoted in different units; the molar mass converts between them.",
+  "type": "number"
+}

Added value: +{
+  "default": "nM",
+  "description": "Unit for targetConcentration.",
+  "enum": [
+    "nM",
+    "uM",
+    "ngPerUl"
+  ],
+  "type": "string"
+}

Added value: +{
+  "default": 20,
+  "description": "Final volume of the diluted sample, in µL.",
+  "type": "number"
+}

Previous value: -"Bases to put in place of the deleted span (delins edit). Omit for a pure deletion."New value: +"Bases to put in place of the deleted span (delins edit). Omit for a pure deletion. NOTE the convention when deleteLength is 0: the insert lands immediately BEFORE `position`, so position 101 + insert \"GGA\" is the same edit as mutation: \"c.100_101insGGA\" — HGVS names the two flanking bases, this names the base the insert sits in front of. `interpretedAs` states which bases the insert ended up between."

Previous value: -"1-based position to substitute (nt), or the first base of the span to replace (delins)."New value: +"1-based position to substitute (nt), or the first base of the span to replace (delins). Required for those forms — it is never assumed. For a pure insertion (deleteLength 0) it is the base the insert goes in FRONT of."

Added value: +{
+  "default": 50000,
+  "description": "Ignore predicted products longer than this (bp). A SEARCH WINDOW, not a claim about what amplifies: whole-plasmid inverse PCR — the reaction a q5-style site_directed_mutagenesis design is run as — makes one product the size of the plasmid, so raise this for a construct over 50 kb. `suppressedByLength` in the response counts what the window discarded.",
+  "maximum": 500000,
+  "minimum": 1,
+  "type": "integer"
+}

Previous value: -"Primer 2, 5'→3' (order does not matter)."New value: +"Primer 2, 5'→3' (order does not matter). Optional: one primer alone is accepted and reports the products it makes on its own — none, unless the template carries inverted sites it can prime from both ends."

Previous value: -[
-  "template",
-  "forwardPrimer",
-  "reversePrimer"
-]New value: +[
+  "template"
+]

Added value: +{
+  "default": 50,
+  "description": "How far apart two reads' breakpoints may sit and still count as the same event, in bp (default 50). Long-read breakpoints are fuzzy, and microhomology at a real junction moves the split legitimately.",
+  "type": "integer"
+}

Previous value: -"Treat the reference as a circular molecule (plasmid). Reads that straddle its arbitrary linear start are then aligned right through the join instead of being cut short there, so variants in the part that would otherwise be clipped away are actually called. Turn this on for whole-plasmid data — the reads begin wherever the molecule was cut, so most of them cross the join. Reads longer than the reference still get clipped."New value: +"Treat the reference as a circular molecule (plasmid). Reads that straddle its arbitrary linear start are then aligned right through the join instead of being cut short there, so variants in the part that would otherwise be clipped away are actually called. Turn this on for whole-plasmid data — the reads begin wherever the molecule was cut, so most of them cross the join. Reads longer than the reference still get clipped. It also governs structural-variant calling: on a circle an origin-crossing read is contiguous, and only this flag lets it be told apart from a whole-reference duplication."

Added value: +{
+  "default": 50,
+  "description": "Smallest structural variant to report, in bp (default 50). Below this the per-base variant caller already reports the event from inside a single alignment, and on nanopore data the range is mostly the error profile.",
+  "type": "integer"
+}

Added value: +{
+  "default": 3,
+  "description": "Distinct reads that must agree on the same breakpoint before a structural variant (large deletion, duplication, inversion, insertion) is reported. Default 3 — stricter than minSupportingReads on purpose: a single split read is a library-prep chimera or a mapping artefact far more often than it is biology, and chimeras are common enough that two agreeing by chance is likelier than two matching base errors.",
+  "type": "integer"
+}

Added value: +{
+  "default": "auto",
+  "description": "Read type, which selects minimap2's alignment preset. \"auto\" (the default) passes no preset and uses minimap2's own defaults — whose parameters happen to be map-ont's, so nanopore data is already handled; setting \"nanopore\" makes that explicit and pins it. \"pacbio\" uses map-hifi and \"illumina\" uses sr, both of which materially change the result: under the ONT defaults gaps are cheap, so on accurate reads a cluster of mismatches can be reported as a spurious indel. \"sanger\" uses map-hifi with the minimum alignment score returned to 80, because map-hifi's own floor of 200 was chosen for 10-25 kb reads and would leave a short or partly-failed Sanger read unmapped. The preset actually used is reported back as minimap2Preset/alignerArgs so a run can be reproduced. Names are matched ignoring case and punctuation, and the obvious aliases resolve (\"ONT\" and \"map-ont\" to nanopore, \"HiFi\" to pacbio, \"sr\" to illumina); anything unrecognised is rejected rather than silently treated as \"auto\".",
+  "enum": [
+    "auto",
+    "nanopore",
+    "pacbio",
+    "illumina",
+    "sanger"
+  ],
+  "type": "string"
+}

Added value: +{
+  "description": "Template bases to remove, starting at `position` (delins edit). 0 with `insert` set is a pure insertion, placed immediately before `position`.",
+  "type": "integer"
+}

Removed value: -"aa"

Previous value: -"Edit at the nucleotide or amino-acid level."New value: +"Edit level. Normally omitted — it is inferred from the fields you send (newBase means nt, targetAa means aa, insert/deleteLength means delins)."

Previous value: -[
-  "nt",
-  "aa"
-]New value: +[
+  "nt",
+  "aa",
+  "delins"
+]

Previous value: -"1-based position of the first base of codon 1 (editKind='aa')."New value: +"1-based position of the first base of codon 1. Needed whenever the coding sequence does not start at base 1 of the template — a residue number means nothing without it."

Added value: +{
+  "description": "Bases to put in place of the deleted span (delins edit). Omit for a pure deletion.",
+  "type": "string"
+}

Added value: +{
+  "description": "The edit by name — \"E52K\", \"p.Glu52Lys\", \"Q100*\", \"c.155A>G\", \"A155G\", \"c.76_78del\", \"c.76_77insGGA\", \"c.76_78dup\", \"c.76delinsAA\". Replaces the field-by-field forms below. An unprefixed \"A123G\" is a legal reading at BOTH levels; it is resolved by which one matches the template, and refused if both do.",
+  "type": "string"
+}

Previous value: -"Replacement base (editKind='nt')."New value: +"Replacement base (nt edit)."

Previous value: -"Codon-usage table for choosing the new codon (editKind='aa')."New value: +"Codon-usage table for choosing the new codon (aa edit). Latin names and common strain/cell-line names are accepted."

Previous value: -"1-based position to substitute (editKind='nt')."New value: +"1-based position to substitute (nt), or the first base of the span to replace (delins)."

Previous value: -"1-based residue number to change (editKind='aa')."New value: +"1-based residue number to change (aa edit)."

Previous value: -"Target amino acid, one-letter code incl '*' (editKind='aa')."New value: +"Target amino acid, one-letter code incl '*' (aa edit)."