NEXUS SeqFold v0.7 | Validation Workflows

Primer-pair off-target screening

Local FASTA only

Forward primer (5′→3′)

Reverse primer (5′→3′)

Background/reference FASTA (≤500,000 total bp)

Max mismatches / primer

Min product (bp)

Max product (bp)

Provide primers and local FASTA. Screening protects the final 5 nt at each primer 3′ end.

Scope: Searches only the sequences supplied. This is NOT whole-genome Primer-BLAST, Primer3, thermodynamic mismatch modeling or evidence of PCR specificity. Repeat regions and degenerate primers are not supported.

Candidate products

Review in silico

—Observed within provided FASTA

Run an analysis.

Experimental reference-free assembly

2–8 overlapping reads

Paste multi-record FASTA (optional)

Or select AB1 / FASTQ / FASTA files (each ≤1200 base calls)

Minimum overlap (bp)

Minimum overlap identity (%)

Loaded reads

No reads loaded.

Upload reads or load the demo.

Developmental algorithm: Greedy overlap merging with affine-gap scoring and automatic reverse-complement orientation. May misassemble repeats or chimeras; indels and mixed peaks require expert review. Unmatched reads remain separate.

Contig and evidence

Uncertainty retained

—Contig length

—Reads joined

—Ambiguous N

Awaiting assembly.

Compare with independently run RNAfold

Not an RNAfold engine

RNA sequence (≤220 nt)

External dot-bracket, optionally with MFE

External engine / version / settings

Paste actual output from a separately run RNAfold program. No remote network calls are made.

Scientific and IP boundary: The existing SeqFold score is an uncalibrated heuristic, not kcal/mol. ViennaRNA is not bundled in this release. Its license conditions require review before redistribution as an integrated product.

Structure agreement

Base-pair metrics

—Pair F1

—Pair distance

—Pairs matched

Awaiting external reference.

Real instrument-read compatibility check

ABIF / AB1

Choose local AB1 chromatogram file

Open chromatogram workbench ↗

No file selected. Actual instrument files have not been independently validated as a broad test set.

Validation gate: This module verifies readable ABIF base calls and available quality/trace arrays. It does not independently re-call fluorescence peaks or validate consensus accuracy. Compare results to a trusted chromatogram reader and known sample/reference.

AB1 metadata & QC

Local processing

No chromatogram loaded.