The Quanexas Toolbox
Everyday bioinformatics tools, right in your browser.
Thirteen tools for sequences, sequencing data, alignments, the wet lab and statistics. Everything runs on your device — nothing you paste or open is uploaded.
Sequence toolkit
Paste DNA or RNA as raw text or FASTA. Spaces and line numbers are ignored; IUPAC ambiguity codes are supported.
Results appear here as you type.
Translate & ORF finder
Translates all six reading frames with the standard genetic code (NCBI table 1) and lists ORFs from ATG to the first in-frame stop codon.
Six-frame translation and ORFs appear here.
For annotation-grade gene calling, use NCBI ORFfinder or a dedicated gene caller.
k-mer counter
Counts every overlapping word of length k. Windows containing N or other ambiguity codes are skipped. Canonical counting merges each k-mer with its reverse complement.
k-mer counts appear here.
FASTA/FASTQ statistics
Paste records or open a file (.fasta, .fastq, or .gz). Files are read inside your browser and never uploaded.
Summary statistics appear here.
For large datasets, use seqkit stats and FastQC.
Phred quality converter
Q = −10·log10(P). Modern Illumina FASTQ uses Phred+33 encoding; Phred+64 appears only in very old files.
Per-base scores and a quality summary appear here.
SAM flag decoder
The FLAG column (column 2 of a SAM record) packs 12 yes/no properties into one number. Type a value or tick the bits.
Common values
The decoded flag appears here.
CIGAR explainer
The CIGAR string (column 6) describes how a read aligns to the reference. Add the POS value (column 4) to get the alignment end coordinate.
Operations and coordinates appear here.
Pairwise alignment
Global (Needleman–Wunsch) or local (Smith–Waterman) alignment with affine gap penalties. A gap of length L costs open + (L−1)×extend; end gaps are penalised.
The alignment appears here.
Defaults mirror EMBOSS Needle and Water. For database searches use BLAST; for many sequences use a multiple aligner such as MAFFT.
Restriction site finder
Finds recognition sites for 20 common enzymes on a linear sequence and predicts the fragments from a digest with the selected enzymes.
Cut sites and fragments appear here.
Methylation sensitivity and star activity are not modelled. For full enzyme databases use NEBcutter.
Primer analyser
Nearest-neighbour Tm (SantaLucia 1998 parameters with a sodium correction) plus common design checks. Guidance only: always confirm with your polymerase supplier’s calculator.
Primer properties appear here.
To design primers against a template, use Primer3 or Primer-BLAST.
Nucleic acid calculator
Molecular weights use the NEBioCalculator formulas, for example dsDNA = (bp × 617.96) + 36.04 g/mol.
Mass → moles & copies
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Moles → mass
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ng/µL → nM
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Dilution: C₁V₁ = C₂V₂
Fill in any three values; the fourth is calculated. Use the same units on both sides.
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A260 → concentration
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Compare with NEBioCalculator, which uses the same formulas.
Multiple-testing correction
Testing thousands of genes at once produces false positives by chance. Bonferroni controls the family-wise error rate; Benjamini–Hochberg controls the false discovery rate (FDR).
Adjusted p-values appear here.
Equivalent to R’s p.adjust(p, "bonferroni") and p.adjust(p, "BH").
Protein properties
Uses the same methods as Biopython’s ProtParam module: average residue masses, Bjellqvist-style pK values for the isoelectric point and the Kyte–Doolittle hydropathy scale.
Protein properties appear here.
Compare with ExPASy ProtParam. Values are estimates from sequence alone and ignore modifications.
Keep learning
Know what the numbers mean.
Every tool links to the concepts behind it in our learning levels, file-format guide and glossary.