# Sequence tools

> Paste a DNA, RNA or protein sequence: reverse complement, six-frame translation and open reading frames, GC content, restriction sites, protein mass and…

Source: https://khushisingh.in/tools/sequence/
Author: Khushi Singh (khushisingh.in). Licence: CC BY 4.0 for text and original illustrations, unless a credit says otherwise.
Evidence labels used on this site: established, strong evidence, emerging, hypothesis, debated. Where a page has Simple, Curious and Expert versions, all three follow.

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Tools

Paste a DNA, RNA or protein sequence: reverse complement, six-frame translation and open reading frames, GC content, restriction sites, protein mass and extinction coefficient, and primer melting temperatures.

Private by design

Sequences are analysed by your browser only; nothing is sent or saved, so unpublished constructs are safe to paste.

*[Here the web page has an interactive activity; open the source URL to use it.]*

## Notes on the methods

- **Translation** uses the standard genetic code (NCBI table 1). Mitochondrial and some microbial genomes use other codes.
- **Open reading frames** run from ATG to the first stop codon. Real genes may start at other codons, contain introns, or be shorter than the longest ORF.
- **Primer Tm** uses SantaLucia’s 1998 nearest-neighbour values with the salt correction of Primer3, so it is close to Primer3 and Primer-BLAST with the same concentrations. Polymerase suppliers’ calculators often use other values; follow your polymerase’s guide for the annealing temperature.
- **Protein parameters** follow ExPASy ProtParam: average masses and Pace’s extinction coefficients. Measured ε can differ by a few per cent.

## References

1. SantaLucia J Jr. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS 95:1460–1465. [doi:10.1073/pnas.95.4.1460](https://doi.org/10.1073/pnas.95.4.1460)
2. von Ahsen N, Wittwer CT, Schütz E. 2001. Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg²⁺, deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations. Clinical Chemistry 47:1956–1961. [doi:10.1093/clinchem/47.11.1956](https://doi.org/10.1093/clinchem/47.11.1956)
3. Untergasser A, et al. 2012. Primer3—new capabilities and interfaces. Nucleic Acids Research 40:e115. [doi:10.1093/nar/gks596](https://doi.org/10.1093/nar/gks596)
4. Pace CN, Vajdos F, Fee L, Grimsley G, Gray T. 1995. How to measure and predict the molar absorption coefficient of a protein. Protein Science 4:2411–2423. [doi:10.1002/pro.5560041120](https://doi.org/10.1002/pro.5560041120)
5. Gasteiger E, et al. 2005. Protein identification and analysis tools on the ExPASy server. In: The Proteomics Protocols Handbook, 571–607. Humana Press. [doi:10.1385/1-59259-890-0:571](https://doi.org/10.1385/1-59259-890-0:571)
6. Prasher DC, Eckenrode VK, Ward WW, Prendergast FG, Cormier MJ. 1992. Primary structure of the Aequorea victoria green-fluorescent protein. Gene 111:229–233. (The example sequence, ENA/GenBank M62653.1.) [doi:10.1016/0378-1119(92)90691-H](https://doi.org/10.1016/0378-1119(92)90691-H)