Reference checks

Reference checks: Drybench Plasmid

This page lists the reference checks published for Drybench Plasmid. Each set gives the methods it covers, what the expected values were computed with, the number of cases, the tolerance the app must meet, the date, and the file holding the inputs and expected outputs, so you can open a case and compare it with what the app gives.

Every case was chosen and recorded by the Drybench team; none has been independently reviewed. A reference check tests the calculation, not your data, your experiment or whether a model suits it. Methods without a set are listed on the methods page with their level.

Methods and levels Documentation

The .dna file set uses synthetic files built from NCBI records only; files saved by other programs are checked at a later pass.

Published sets

Published verification sets

Methods	Oracle	Fixtures	Tolerance	Date	File
sequence-primer-features	Independent Sequence handoff	43	full incorporated PCR primers, exact witnessed template sites, wrapped strands, refusal and omission counts exact; supplied annotations preserved	2026-10-11	sequence-handoff-v1.jsonRecorded for version 0.12.0; the test suite checks the current engine against it.
ds-fragment-ends, restriction-cloning, golden-gate	Biopython	67	strand chemistry and paired cores exact; circular products identical up to rotation and strand; overlapping cuts refused	2026-10-11	assembly-boundaries.jsonRecorded for version 0.9.0; the test suite checks the current engine against it.
ds-fragment-ends, restriction-cloning	Biopython	1	coincident top cuts with distinct opposite-strand cuts refused	2026-10-11	assembly-cut-refusals-v1.jsonRecorded for version 0.10.0; the test suite checks the current engine against it.
assembly-record	Independent assembly records	10	shape, exact hashes, topology, parent references and method-specific accounting; malformed provenance refused, stale provenance dropped with reason	2026-10-11	assembly-record-v2.jsonRecorded for version 0.9.0; the test suite checks the current engine against it.
assembly-record	Independent assembly records	19	exact input/junction totals, parent roles, junction counts and method-specific alternatives; balanced false claims refused	2026-10-11	assembly-record-refusals-v1.jsonRecorded for version 0.11.0; the test suite checks the current engine against it.
restriction-sites, restriction-digest	Biopython	446	cut positions and fragment lengths exact; the unique-cutter sets identical	2026-10-06	digests.jsonRecorded for version 0.1.0; the test suite checks the current engine against it.
dam-dcm-blocking	McClelland et al. 1994, Table I	21	outcomes exact	2026-10-06	methylation.jsonRecorded for version 0.1.0; the test suite checks the current engine against it.
diagnostic-digest-picker	Biopython	4157	the pool, bands and verdicts exact (gel rules 2)	2026-10-17	trio-v2.jsonRecorded for version 0.13.0; the test suite checks the current engine against it.
gel-schematic	Hand-worked band grouping	11	bands exact	2026-10-17	gel-bands-v1.jsonRecorded for version 0.13.0; the test suite checks the current engine against it.
feature-annotation	Biopython	38	identity and coverage within 0.1 percentage points; place, strand, call and score exact	2026-10-06	features.jsonRecorded for version 0.1.0; the test suite checks the current engine against it.
feature-annotation	Biopython	4017	every pair of library 2's parts aligned with the same scoring: calls, places, strands and buckets exact; no call on the random controls	2026-10-17	specificity-v2.jsonRecorded for version 0.14.0; the test suite checks the current engine against it.
feature-annotation	Biopython	14	the call shown at each locus, the parts named beside it and the inside labels exact	2026-10-17	specificity-display.jsonRecorded for version 0.14.0; the test suite checks the current engine against it.
dam-dcm-blocking	Independent second implementation (reference.py can_carry)	82	which enzymes' sites can carry a dam or dcm methylated base, exact; whether Table I lists the enzymes without a row is not checked	2026-10-17	methylation-absence-rule.jsonRecorded for version 0.14.0; the test suite checks the current engine against it.
plasmid-dna-amounts	Python fractions	11	full double precision (1e-12 relative)	2026-10-06	amounts.jsonRecorded for version 0.1.0; the test suite checks the current engine against it.
snapgene-read	Biopython	10	sequence and topology identical; every feature recovered; refusals for the stated reason	2026-10-06	dna-files.jsonRecorded for version 0.1.0; the test suite checks the current engine against it.
ds-fragment-ends	Hand-worked double-stranded ends	13	every overhang, polarity and compatibility verdict exact	2026-10-10	ds-ends.jsonRecorded for version 0.7.0; the test suite checks the current engine against it.
restriction-cloning	Hand-worked restriction clones	5	every product exact up to rotation and strand; refusals for the stated reason; material conserved	2026-10-10	restriction-cloning.jsonRecorded for version 0.3.0; the test suite checks the current engine against it.
golden-gate	Hand-worked Golden Gate assemblies	7	the scarless product exact up to rotation and strand, no recognition site surviving; refusals for the stated reason	2026-10-10	golden-gate.jsonRecorded for version 0.7.0; the test suite checks the current engine against it.
gibson-style	Hand-worked Gibson assemblies	7	the product exact (a circle up to rotation and strand), each overlap collapsed once, material conserved; refusals for the stated reason	2026-10-10	gibson.jsonRecorded for version 0.7.0; the test suite checks the current engine against it.
crispr-spcas9-guides	Independent SpCas9 enumeration	21	every position, strand, protospacer, PAM, GC, homopolymer run, within-sequence count and origin crossing exact; no score	2026-10-10	crispr.jsonRecorded for version 0.7.0; the test suite checks the current engine against it.

Oracles and build-time tools

Software the app's numbers were checked against, or its data built with. None of it ships with the app or is a dependency of it.

Independent Sequence handoff sequence-handoff.py with Biopython 1.88 (MIT (script); Biopython License Agreement; Oracle; 2026-10-11). independently re-extracted product and template footprints, paired omissions, immutable qualifications and malformed receipt refusals
Independent assembly records assembly-boundaries.py (MIT; Oracle; 2026-10-11). hand-authored record cases based on previously published independent products, with Python hashlib hashes and method-specific conservation
Biopython 1.88 (Biopython Licence Agreement or BSD-3-Clause; Oracle; 2026-10-06). Bio.Restriction to check every enzyme row and cut position, PairwiseAligner for the feature alignments, and the SnapGene reader for the synthetic .dna files; never shipped
Independent second implementation (reference.py can_carry) reference.py absences (MIT; Oracle; 2026-10-17). which enzymes' sites can carry a dam or dcm methylated base, by expanding each site's IUPAC codes; shares no code with the engine and calls no Biopython
Python fractions 3.11 (PSF-2.0; Oracle; 2026-10-06). exact arithmetic for the bench numbers
Hand-worked band grouping reference.py gel (MIT; Oracle; 2026-10-17). band-grouping cases worked by hand with exact fractions
McClelland et al. 1994, Table I Nucleic Acids Res 22:3640 (Cited data (read by hand); Oracle; 2026-10-06). the methylation outcomes, each case worked by hand from the table's entries
Hand-worked double-stranded ends ds-ends.py with Biopython 1.88 (MIT (the script); Biopython Licence Agreement (BSD-3-Clause file by file); Oracle; 2026-10-10). the overhang, polarity and compatibility of restriction ends, each case worked by hand and re-derived from a two-strand drawing
Hand-worked restriction clones restriction-cloning.py with Biopython 1.88 (MIT (the script); Biopython Licence Agreement (BSD-3-Clause file by file); Oracle; 2026-10-10). recombinant products worked out by hand and round-tripped by Bio.Restriction, which digests each product back into the insert and backbone cores; reverse complements by Biopython
Hand-worked Golden Gate assemblies golden-gate.py with Biopython 1.88 (MIT (the script); Biopython Licence Agreement (BSD-3-Clause file by file); Oracle; 2026-10-10). BsaI and BsmBI assemblies built around a chosen scarless product; Bio.Restriction confirms the released overhangs and that no recognition site survives in the product; reverse complements by Biopython
Hand-worked Gibson assemblies gibson.py with Biopython 1.88 (MIT (the script); Biopython Licence Agreement (BSD-3-Clause file by file); Oracle; 2026-10-10). exact-overlap assemblies built from a chosen product; the product is re-derived by an independent concatenation and base-accounted; reverse complements by Biopython
Independent SpCas9 enumeration crispr.py with Biopython 1.88 (MIT (the script); Biopython Licence Agreement (BSD-3-Clause file by file); Oracle; 2026-10-10). every NGG guide found by one regular-expression search for a protospacer and its PAM, run over the sequence for the + strand and over the Biopython reverse complement for the − strand with positions mapped back, one case worked by hand base by base with a write-refusal guard, and GC, homopolymer run and the within-sequence occurrence count computed independently; no score

Fixture tables, computed when the page was built

Every row is one fixture compared with the engine when this page was built; the full sets are the published files, which pipeline/plasmid-map/reference.py wrote and whose hashes its manifest records. No value in a file comes from the engine under test.

Every enzyme's cut positions and fragments on pUC19 and pBR322, and the double digests

Biopython 1.88 Bio.Restriction (REBASE release 404, an offline oracle); tolerance: exact. 458 cases, all passing; the first 12 shown. digests.json sha256 4b39c25d5bb5f091

Uses no annotation library.

Case	Oracle	This engine	Pass
AarI on L09137.2	no site	no site	yes
AarI on J01749.1	no site	no site	yes
AatII on L09137.2	cuts after 2,622	cuts after 2,622	yes
AatII on J01749.1	cuts after 4,289	cuts after 4,289	yes
AbsI on L09137.2	no site	no site	yes
AbsI on J01749.1	no site	no site	yes
Acc65I on L09137.2	cuts after 409	cuts after 409	yes
Acc65I on J01749.1	no site	no site	yes
AccI on L09137.2	cuts after 431	cuts after 431	yes
AccI on J01749.1	cuts after 653, 2,246	cuts after 653, 2,246	yes
AciI on L09137.2	cuts after 76, 115, 125, 151, 189, 202, 228, 285, 497, 600, 656, 666, 690, 733, 740, 761, 852, 880, 1,007, 1,026, 1,147, 1,257, 1,392, 1,401, 1,763, 1,854, 2,045, 2,091, 2,212, 2,256, 2,333, 2,442, 2,541, 2,588	cuts after 76, 115, 125, 151, 189, 202, 228, 285, 497, 600, 656, 666, 690, 733, 740, 761, 852, 880, 1,007, 1,026, 1,147, 1,257, 1,392, 1,401, 1,763, 1,854, 2,045, 2,091, 2,212, 2,256, 2,333, 2,442, 2,541, 2,588	yes
AciI on J01749.1	cuts after 40, 182, 290, 299, 302, 426, 579, 582, 585, 704, 724, 803, 843, 892, 939, 1,024, 1,039, 1,107, 1,140, 1,165, 1,210, 1,234, 1,246, 1,288, 1,342, 1,395, 1,411, 1,417, 1,498, 1,636, 1,765, 1,768, 1,779, 1,935, 1,951, 2,006, 2,062, 2,147, 2,186, 2,196, 2,238, 2,263, 2,301, 2,314, 2,340, 2,357, 2,400, 2,407, 2,428, 2,519, 2,547, 2,674, 2,693, 2,814, 2,924, 3,059, 3,068, 3,430, 3,521, 3,712, 3,758, 3,879, 3,923, 4,000, 4,109, 4,208, 4,255	cuts after 40, 182, 290, 299, 302, 426, 579, 582, 585, 704, 724, 803, 843, 892, 939, 1,024, 1,039, 1,107, 1,140, 1,165, 1,210, 1,234, 1,246, 1,288, 1,342, 1,395, 1,411, 1,417, 1,498, 1,636, 1,765, 1,768, 1,779, 1,935, 1,951, 2,006, 2,062, 2,147, 2,186, 2,196, 2,238, 2,263, 2,301, 2,314, 2,340, 2,357, 2,400, 2,407, 2,428, 2,519, 2,547, 2,674, 2,693, 2,814, 2,924, 3,059, 3,068, 3,430, 3,521, 3,712, 3,758, 3,879, 3,923, 4,000, 4,109, 4,208, 4,255	yes

dam and dcm outcomes, worked by hand

McClelland et al. 1994, Table I; tolerance: exact. 19 cases, all passing; the first 12 shown. methylation.json sha256 3b72a819ada98d26

Uses no annotation library.

Case	Oracle	This engine	Pass
M01: XbaI, dam on, dcm on	cut	cut	yes
M02: XbaI, dam on, dcm on	blocked	blocked	yes
M03: XbaI, dam on, dcm on	blocked	blocked	yes
M04: BamHI, dam on, dcm on	not-blocked	not-blocked	yes
M05: BsaWI, dam on, dcm on	not-recorded	not-recorded	yes
M06: AhdI, dam on, dcm on	not-recorded	not-recorded	yes
M07: EcoRII, dam on, dcm on	blocked	blocked	yes
M08: BstNI, dam on, dcm on	not-blocked	not-blocked	yes
M09: StuI, dam on, dcm on	blocked	blocked	yes
M10: XbaI, dam on, dcm on	blocked	blocked	yes
M11: BglI, dam on, dcm on	not-recorded	not-recorded	yes
M12: DpnI, dam on, dcm on	cuts-methylated	cuts-methylated	yes

The digest picker on the correct, empty and reversed trio (trio v2, gel rules 2)

Biopython 1.88 Bio.Restriction; tolerance: the pool, every band and every verdict exact. 4,158 cases, all passing; the first 12 shown. trio-v2.json sha256 fd62948a014229b7

Uses no annotation library.

Case	Oracle	This engine	Pass
the constructs and the pool	95 enzymes; the constructs' SHA-256	95 enzymes; the same constructs	yes
AatII	does not	does not	yes
Acc65I	does not	does not	yes
AccI	does not	does not	yes
AclI	does not	does not	yes
AcuI	tells all three apart	tells all three apart	yes
AflIII	does not	does not	yes
AhdI	does not	does not	yes
AlwNI	does not	does not	yes
ApaLI	does not	does not	yes
ApoI	does not	does not	yes
AseI	does not	does not	yes

Band grouping on the schematic gel, worked by hand

Hand-worked cases with exact fractions; tolerance: every band exact; the 5 percent boundary inclusive. 11 cases, all passing; the first 11 shown. gel-bands-v1.json sha256 565950590c2bf04a

Uses no annotation library.

Case	Oracle	This engine	Pass
chain-1000-960-922: 1000, 960, 922 bp	[1000, 960] [922]	[1000, 960] [922]	yes
boundary-inclusive: 1000, 950 bp	[1000, 950]	[1000, 950]	yes
boundary-just-over: 1000, 949 bp	[1000] [949]	[1000] [949]	yes
four-member-run: 2000, 1980, 1950, 1900 bp	[2000, 1980, 1950, 1900]	[2000, 1980, 1950, 1900]	yes
long-run-splits: 2000, 1960, 1920, 1880, 1840 bp	[2000, 1960, 1920] [1880, 1840]	[2000, 1960, 1920] [1880, 1840]	yes
under-100-not-drawn: 3000, 100, 99, 60 bp	[3000] [100]	[3000] [100]	yes
near-100: 105, 100 bp	[105, 100]	[105, 100]	yes
equal-sizes: 500, 500, 500 bp	[500, 500, 500]	[500, 500, 500]	yes
equal-then-boundary: 1000, 1000, 950, 949 bp	[1000, 1000, 950] [949]	[1000, 1000, 950] [949]	yes
unsorted-input: 922, 1000, 960 bp	[1000, 960] [922]	[1000, 960] [922]	yes
all-under-100: 99, 50, 10 bp	no band	no band	yes

Feature alignments and threshold boundaries

Biopython 1.88 PairwiseAligner; tolerance: identity and coverage within 0.1 percentage points; place, call and score exact. 26 cases, all passing; the first 12 shown. features.json sha256 a523a03a76efcc1a

Checked against annotation library 1.

Case	Oracle	This engine	Pass
F01: bla on X65304.3	match, 99.77% identity, 100.00% coverage at 1265	match, 99.77% identity, 100.00% coverage at 1265	yes
F02: bla on U47120.2	match, 99.77% identity, 100.00% coverage at 3780	match, 99.77% identity, 100.00% coverage at 3780	yes
F03: bla on AF025843.2	match, 99.77% identity, 100.00% coverage at 2393	match, 99.77% identity, 100.00% coverage at 2393	yes
F04: bla on U13853.1	match, 100.00% identity, 100.00% coverage at 1377	match, 100.00% identity, 100.00% coverage at 1377	yes
F05: nptII on U55762.1	match, 99.75% identity, 100.00% coverage at 2629	match, 99.75% identity, 100.00% coverage at 2629	yes
F06: nptII on U47120.2	match, 100.00% identity, 100.00% coverage at 2463	match, 100.00% identity, 100.00% coverage at 2463	yes
F07: nptII on AY048743.1	match, 100.00% identity, 100.00% coverage at 459	match, 100.00% identity, 100.00% coverage at 459	yes
F08: cat on LC760188.1	match, 100.00% identity, 100.00% coverage at 3344	match, 100.00% identity, 100.00% coverage at 3344	yes
F09: lacI on U13853.1	match, 99.91% identity, 100.00% coverage at 3318	match, 99.91% identity, 100.00% coverage at 3318	yes
F10: egfp on U55763.1	match, 100.00% identity, 99.72% coverage at 613	match, 100.00% identity, 99.72% coverage at 613	yes
F11: cmvEnhancer on AF025843.2	match, 99.85% identity, 99.85% coverage at 7	match, 99.85% identity, 99.85% coverage at 7	yes
F12: cmvPromoter on AF025843.2	match, 100.00% identity, 100.00% coverage at 667	match, 100.00% identity, 100.00% coverage at 667	yes

ng, pmol, copies, ligation and the weights

Python fractions (exact arithmetic); tolerance: 1e-12 relative. 11 cases, all passing; the first 11 shown. amounts.json sha256 b796d93baed8c741

Uses no annotation library.

Case	Oracle	This engine	Pass
A01: pmol	0.6025208835093896	0.6025208835093896	yes
A02: pmol	0.18554121286562347	0.18554121286562347	yes
A03: copies-per-ul	3628465571.333107	3628465571.333107	yes
A04: copies-per-ul	223471060.13158152	223471060.13158152	yes
A05: ligation-insert-ng	40.20848845867461	40.20848845867461	yes
A06: ligation-insert-ng	26.805658972449738	26.80565897244974	yes
A07: ligation-insert-ng	57.32630130703967	57.32630130703967	yes
A08: pmol-approximate	0.5727704908643106	0.5727704908643106	yes
A09: ng-for-copies	27.559859128898875	27.559859128898875	yes
A10: mw	1659693.51	1659693.51	yes
A11: mw	2694819.077	2694819.077	yes

Synthetic .dna files and refusals

Biopython 1.88 SnapGene reader; tolerance: sequence and topology identical; every feature recovered; refusals for the stated reason. 10 cases, all passing; the first 10 shown. dna-files.json sha256 74f5f2b35995cb89

Uses no annotation library.

Case	Oracle	This engine	Pass
dna/refuse-length-mismatch.dna	refused: length-mismatch	refused: length-mismatch	yes
dna/refuse-truncated.dna	refused: truncated	refused: truncated	yes
dna/refuse-unknown-packet.dna	refused: unknown-packet	refused: unknown-packet	yes
dna/refuse-unknown-version.dna	refused: unknown-version	refused: unknown-version	yes
dna/synthetic-2micron-origin.dna	6318 bp circular; 40 features	6318 bp circular; 40 of 40 recovered	yes
dna/synthetic-lac-linear.dna	7477 bp linear; 15 features	7477 bp linear; 15 of 15 recovered	yes
dna/synthetic-pbr322.dna	4361 bp circular; 46 features	4361 bp circular; 46 of 46 recovered	yes
dna/synthetic-pcineo.dna	5472 bp circular; 13 features	5472 bp circular; 13 of 13 recovered	yes
dna/synthetic-pgem3z-origin.dna	2743 bp circular; 13 features	2743 bp circular; 13 of 13 recovered	yes
dna/synthetic-puc19-linear.dna	2686 bp linear; 0 features	2686 bp linear; 0 of 0 recovered	yes

The GenBank export read back

Biopython 1.88 GenBank parser; tolerance: translations equal or refused alike; ACCESSION '.'; no identifier on a person's feature. 11 cases, all passing; the first 11 shown. genbank.json sha256 da83de6798455d21

Uses no annotation library.

Case	Oracle	This engine	Pass
pbr322-edits CDS 1 (edited)	Biopython refuses	none written (Final codon 'ATG' is not a stop codon)	yes
pbr322-edits CDS 2 (library)	Biopython's translation	/translation written	yes
pbr322-edits CDS 3 (edited)	Biopython's translation	/translation written	yes
pbr322-edits CDS 4 (as received)	Biopython's translation	/translation written	yes
pbr322-edits CDS 5 (added)	Biopython refuses	none written (First codon 'ACC' is not a start codon)	yes
pbr322-edits CDS 6 (library)	Biopython's translation	/translation written	yes
pbr322-edits CDS 7 (as received)	Biopython's translation	/translation written	yes
puc19-edits misc_feature 1 (added)	ASCII notes, no identifier	ASCII notes, no identifier	yes
puc19-edits CDS 2 (edited)	Biopython's translation	/translation written	yes
puc19-edits CDS 3 (added)	Biopython refuses	none written (First codon 'GAG' is not a start codon)	yes
puc19-edits CDS 4 (added)	Biopython refuses	none written (Final codon 'TGG' is not a stop codon)	yes

The worked examples' golden fixtures (every file the examples manifest lists, published beside it)

Biopython 1.88; tolerance: exact. 30 cases, all passing; the first 12 shown. examples-manifest.json sha256 791b9d3b5df5cdec

Each file is checked against its own annotation library: library 1 for puc19@1.json and pbr322@1.json; library 2 for puc19@2.json and pbr322@2.json and pbluescript-sk@1.json and pbluescript-ks@1.json and pgem-3z@1.json and pacyc184@1.json and pegfp-n1@1.json and pgex-4t-1@1.json.

Case	Oracle	This engine	Pass
puc19@1.json: calls and UniProt checks	6 calls	6 calls	yes
puc19@1.json: primer sites	4	4	yes
puc19@1.json: cut counts	223 enzymes	223 agree	yes
pbr322@1.json: calls and UniProt checks	4 calls	4 calls	yes
pbr322@1.json: primer sites	0	0	yes
pbr322@1.json: cut counts	223 enzymes	223 agree	yes
puc19@2.json: calls and UniProt checks	7 calls	7 calls	yes
puc19@2.json: primer sites	4	4	yes
puc19@2.json: cut counts	223 enzymes	223 agree	yes
pbr322@2.json: calls and UniProt checks	5 calls	5 calls	yes
pbr322@2.json: primer sites	0	0	yes
pbr322@2.json: cut counts	223 enzymes	223 agree	yes