workbench

 ⟨34 unchanged words⟩  used, °C. Compared against each primer's own nearest-neighbournearest-neighbor Tm.","type":"number"},"colonies" ⟨35 unchanged words⟩ the insert and vector were cut with. An unrecognisedunrecognized name is rejected rather than skipped: every  ⟨748 unchanged words⟩ 

 ⟨34 unchanged words⟩  used, °C. Compared against each primer's own nearest-neighbournearest-neighbor Tm.","type":"number"},"colonies" ⟨35 unchanged words⟩ the insert and vector were cut with. An unrecognisedunrecognized name is rejected rather than skipped: every  ⟨748 unchanged words⟩ 

 ⟨30 unchanged words⟩ methods — the junction primers. Each method is modelledmodeled as its own chemistry rather than as one ⟨48 unchanged words⟩ 

 ⟨602 unchanged words⟩  topo and lic methods; for lic, the LINEARISEDLINEARIZED vector).","type":"string"}," ⟨95 unchanged words⟩ 

CAI analyseranalyzer

 ⟨3 unchanged words⟩ :false,"readOnlyHint":true,"title":"CAI analyseranalyzer"}

Codon optimiseroptimizer

Codon-optimiseCodon-optimize a protein (or coding DNA) for an ⟨9 unchanged words⟩ 

 ⟨76 unchanged words⟩  (residues after an in-frame stop are NOT optimisedoptimized).","type":"string"}},"required ⟨3 unchanged words⟩ 

 ⟨3 unchanged words⟩ :false,"readOnlyHint":true,"title":"Codon optimiseroptimizer"}

 ⟨27 unchanged words⟩  enzymes (BsaI, BbsI, Esp3I/BsmBI); an unrecognisedunrecognized name is rejected, never skipped.","items" ⟨102 unchanged words⟩ 

 ⟨285 unchanged words⟩ U6/Pol III promoter; the authors expect it to generalisegeneralize less well to Pol II-transcribed sgRNAs, and  ⟨59 unchanged words⟩ 

 ⟨122 unchanged words⟩ is the whole curated set of 49. An unrecognisedunrecognized name is rejected rather than skipped, so  ⟨69 unchanged words⟩ 

 ⟨73 unchanged words⟩ , because negatives are clamped to zero during normalisationnormalization and a baseline-subtracted trace would silently lose its ⟨760 unchanged words⟩ 

 ⟨9 unchanged words⟩ , rather than scoring one you already have. MaximisesMaximizes the fidelity of the set's WEAKEST junction against ⟨92 unchanged words⟩ 

 ⟨25 unchanged words⟩ ,"description":"Which real ligation dataset to optimiseoptimize against.","enum":["generic-t4-37c-1h","bsai-hfv2" ⟨173 unchanged words⟩ 

 ⟨5 unchanged words⟩ :true,"description":"Engineer the internal ARMS destabilisingdestabilizing mismatch near the 3' end.","type": ⟨135 unchanged words⟩ 

Primer/oligo melting temperature: nearest-neighbournearest-neighbor (SantaLucia 1998) at the supplied reaction conditions ⟨21 unchanged words⟩ 

Full oligo analysis: nearest-neighbournearest-neighbor Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings.

 ⟨187 unchanged words⟩ know your primer concentration, salt, or cycling programmeprogram, so it cannot say whether a dimer  ⟨6 unchanged words⟩ 

 ⟨46 unchanged words⟩ ":{"description":"Second oligo. Omit to analyseanalyze hairpin structure in 'a' alone; pass the same ⟨60 unchanged words⟩ 

 ⟨128 unchanged words⟩ multiplex panel designer uses. Every number is a nearest-neighbournearest-neighbor calculation over the sequences supplied, not a  ⟨7 unchanged words⟩ 

 ⟨90 unchanged words⟩ ":"global","description":"\"global\" penalisespenalizes end gaps in both sequences; \"local\"  ⟨78 unchanged words⟩ 

 ⟨7 unchanged words⟩ every feature with its span, strand, display colourcolor and qualifiers (spliced and origin-spanning features kept  ⟨7 unchanged words⟩ 

 ⟨161 unchanged words⟩ and efficiency ranking within one locus. It is parameterisedparameterized on HEK293 and K562; your cell type,  ⟨34 unchanged words⟩ 

 ⟨120 unchanged words⟩ at the extending end — with that anchor's nearest-neighbournearest-neighbor ΔG and a margin against the intended,  ⟨201 unchanged words⟩ 

 ⟨169 unchanged words⟩  E. coli-like Gram-negative hosts (the model is parameterisedparameterized on the E. coli anti-Shine-Dalgarno sequence). Rankings ⟨13 unchanged words⟩ 

 ⟨33 unchanged words⟩  the full thermodynamic breakdown (16S rRNA:mRNA hybridisationhybridization, mRNA unfolding, spacing, standby site, start-codon ⟨107 unchanged words⟩  E. coli-like Gram-negative hosts (the model is parameterisedparameterized on the E. coli anti-Shine-Dalgarno sequence). Rankings ⟨13 unchanged words⟩ 

 ⟨120 unchanged words⟩  fixed 37 °C. No pseudoknots, no two-strand hybridisationhybridization, and no temperature dependence — a structure  ⟨10 unchanged words⟩ 

 ⟨254 unchanged words⟩ read is a library-prep chimera or a mapping artefactartifact far more often than it is biology,  ⟨173 unchanged words⟩ pacbio, \"sr\" to illumina); anything unrecognisedunrecognized is rejected rather than silently treated as \ ⟨110 unchanged words⟩ 

 ⟨29 unchanged words⟩  on siDirect's own RNA/RNA scale: Freier 1986 nearest-neighbournearest-neighbor parameters, helix initiation A = −10.8, CT ⟨57 unchanged words⟩ claimed for the ranking. Target-site accessibility is not modelledmodeled (no folding) and no transcriptome-wide off-target search ⟨61 unchanged words⟩ 

 ⟨4 unchanged words⟩ default":true,"description":"Engineer the ARMS destabilisingdestabilizing mismatch 3 nt from the allele-specific primer's 3' ⟨477 unchanged words⟩ 

 ⟨44 unchanged words⟩  the vector name, or the accession. An unrecognisedunrecognized id is an error carrying the closest names ⟨5 unchanged words⟩ 

 ⟨57 unchanged words⟩  A curated public-record set, NOT a vendor cataloguecatalog — see the gate's notChecked.

 ⟨122 unchanged words⟩ ":{"default":false,"description":"The linearisedlinearized vector was CIP/rSAP-dephosphorylated (restriction method). Affects  ⟨545 unchanged words⟩ (restriction and lic methods; for lic, the LINEARISEDLINEARIZED vector). Omit if vectorPcr is given.", ⟨118 unchanged words⟩ 

 ⟨28 unchanged words⟩ see restriction_sites for the full list). An unrecognisedunrecognized name is rejected rather than skipped, so  ⟨54 unchanged words⟩ 

 ⟨32 unchanged words⟩ :5,"description":"Up to 20.","maximum":20,"minimum":1,"type":"integer"},"organism":{"description" ⟨41 unchanged words⟩ 

 ⟨55 unchanged words⟩  A, C, G, T/U only. Max 310,000 nt.","type":"string"}," ⟨111 unchanged words⟩ 

 ⟨75 unchanged words⟩  A, C, G, T/U only. Max 310,000 nt.","type":"string"}," ⟨20 unchanged words⟩