Sequence Analysis Tools
These tools work on the sequence itself: paste in DNA, RNA or protein, get a different representation, a property, or a site.
Where to start: with a raw DNA fragment, settle orientation and composition first using reverse complement and sequence statistics; to express it, confirm the reading frame with six-frame translation; to clone it, check cut sites with restriction analysis; to amplify it, use primer Tm and primer dimer.
The recurring trap here is orientation and coordinates. After a reverse complement the strand has flipped, so every position computed on the original strand is void. And genome coordinates come in 0-based and 1-based conventions — UCSC BED and Ensembl/GFF differ by one, and that one position propagates through everything downstream. Coordinate conversion exists for exactly this.
Two tools people confuse: the codon table answers “what does this triplet encode”, while codon usage answers “how often is this triplet used in this host”. The first is the genetic code, the second is species preference — heterologous expression needs the second.
Everything is processed in your own browser. Nothing is uploaded or stored, so unpublished sequences are safe to paste.
Sequence tools
DNA / RNA Reverse Complement Online Converter
Paste a sequence to get its reverse complement, complement, or reverse; supports FASTA input and IUPAC degenerate bases.
Online DNA GC Content and Tm Calculator
Calculate GC%, base composition, molecular weight, and two empirical Tm values — for rapid primer screening.
DNA to Protein Translation — Six-Frame Online Tool
Standard genetic code (NCBI table 1): single-frame or six-frame translation with ORF finder.
FASTA File Statistics: Sequence Count, Length Distribution, and N50
Paste a multi-FASTA and instantly get sequence count, total length, N50/L50, GC content, and length distribution.
Protein Molecular Weight, Isoelectric Point & 280 nm Extinction Coefficient Calculator
Enter an amino acid sequence to compute molecular weight, theoretical pI, molar extinction coefficient, and A280 at 1 mg/mL.
Pairwise Sequence Alignment Online Tool (Needleman-Wunsch Global Alignment)
Global alignment of two sequences with alignment output, score, percent identity, and mismatch/gap statistics.
Codon Table Quick Reference (Standard Genetic Code): Bidirectional Codon–Amino Acid Lookup
All 64 codons of the standard genetic code — look up amino acids by codon or reverse-query codons by amino acid; accepts both DNA and RNA notation.
Amino Acid Properties Reference: Molecular Weight, Side-Chain pKa, Hydrophobicity, and Codon Count
Properties of all 20 standard amino acids: residue mass, side-chain pKa, Kyte-Doolittle hydrophobicity, and codon count. Searchable by code or name.
Restriction Enzyme Recognition Sequences Reference & Cut-Site Finder
Recognition sequences, cut sites, end types, and average spacing for 30 common restriction enzymes; paste any sequence to locate cut sites (linear or circular).
Non-Standard Genetic Code Tables: Mitochondrial, Bacterial, and Ciliate Codon Differences (NCBI transl_table Reference)
All 27 NCBI genetic code tables with per-codon differences from the standard table, searchable by table number or codon.
Codon Usage Table & Rare Codon Scanner (with CAI Calculation)
Codon usage frequencies for nine organisms — paste a CDS to scan for rare codons, compute CAI, and identify the optimal codon per amino acid in your expression host.
Primer Dimer and Hairpin Structure Detector (with 3′-End Complementarity Analysis)
Detect self-dimers, hairpin structures, and cross-dimers in primer pairs; reports 3′-end consecutive complementarity separately with a pairing diagram.
Nearest-Neighbor Primer Tm Calculator
Calculate primer Tm by nearest-neighbor thermodynamics, returning ΔH°, ΔS°, ΔG°₃₇, with Mg²⁺ and dNTP converted to Na⁺ equivalent.
FASTQ Quality Score Calculator — Phred Q Score, Error Rate, Q20/Q30
Convert Phred Q scores to error rates and parse FASTQ quality strings: correct mean quality, ≥Q20/Q30 fractions, and expected error count.
Genome Coordinate System Converter — BED (0-based) ↔ GFF/VCF/SAM (1-based)
BED and GFF/VCF/SAM coordinates differ by 1. Convert any interval between the two systems and get ready-to-paste BED and GFF lines.
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