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QUICK PEEKDNA SEQUENCE ANALYSER

DNA GC content calculator, reverse complement and ORF finder.

Paste a DNA sequence to get its length, GC content (G + C as a share of A, C, G and T), base counts and reverse complement. It also lists every open reading frame of 30 nt or more on the forward strand and translates the longest one into protein.

Analyse a sequenceAll quick peeks
NO ACCOUNT · RUNS IN YOUR BROWSER · ABOUT 30 SECONDS
Fig 0DOUBLE HELIX · ORF
ORF · ATG → TAAGCTATGGCCAAGCTGTTCGAGTAAGCA5′3′ATGC
The analyser scans each forward frame from ATG to the first in-frame stop codon.
FIG 1THE PEEK

Paste DNA, read the result.

A sample is pre-filled. Edit it or paste your own; the result updates as you type.

Fig 1DNA · FORWARD STRAND · STANDARD CODE
HEADERS (>), SPACES AND NUMBERS ARE REMOVED · U IS READ AS T · SAMPLE IS ILLUSTRATIVE
REVERSE COMPLEMENT · 5′→3′
TTATTTGTAGAGCTCATCCATGCCATGTGTAATCCCAGCAGCAGTTACAAACTCAAGAAGGACCATGTGGTCACGCTTTTCGTTGGGATCTTTCGAAAGGGCAGATTGTGTCGACAGGTAATGGTTGTCTGGTAAAAGGACAGGGCCATCGCCAATTGGAGTATTTTGTTGATAATGGTCTGCTAGTTGAACGGATCCATCTTCAATGTTGTGGCGAATTTTGAAGTTAGCTTTGATTCCATTCTTTTGTTTGTCTGCCGTGATGTATACATTGTGTGAGTTATAGTTGTACTCGAGTTTGTGTCCGAGAATGTTTCCATCTTCTTTAAAATCAATACCTTTTAACTCGATACGATTAACAAGGGTATCACCTTCAAACTTGACTTCAGCACGCGTCTTGTAGTTCCCGTCATCTTTGAAAGATATAGTGCGTTCCTGTACATAACCTTCGGGCATGGCACTCTTGAAAAAGTCATGCCGTTTCATGTGATCCGGATAACGGGAAAAGCATTGAACACCATAAGAGAAAGTAGTGACAAGTGTTGGCCATGGAACAGGTAGTTTTCCAGTAGTGCAAATAAATTTAAGGGTAAGCTTTCCGTATGTAGCATCACCTTCACCCTCTCCACTGACAGAAAATTTGTGCCCATTAACATCACCATCTAATTCAACAAGAATTGGGACAACTCCAGTGAAAAGTTCTTCTCCTTTGCTAGCCATGGTGGC
THE LINK CONTAINS YOUR INPUTS AND REOPENS THIS RESULT
726
LENGTH · NT
41.9%
GC CONTENT
6
ORFS ≥ 30 NT
239 aa
LONGEST ORF
BASE COMPOSITION
A 228 · 31.4%C 158 · 21.8%G 146 · 20.1%T 194 · 26.7%
OPEN READING FRAMESFORWARD STRAND · ATG → STOP
#FRAMESTART–ENDNTAASTOP
1+17–726720239TAA
2+265–24418059TGA
3+3177–2547825TGA
4+2251–38513544TAA
5+2407–54413845TAG
6+2578–68210534TAA
LONGEST ORF · PROTEIN (239 AA)
MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK
STANDARD CODE (NCBI TABLE 1) · STOP CODON NOT SHOWN · X = CODON WITH N
SEQUENCE · LONGEST ORF HIGHLIGHTED
GCCACCATGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCACATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA
RUNS ENTIRELY IN YOUR BROWSER — NOTHING IS UPLOADED.
FIG 2HOW TO USE

How to use the DNA sequence analyser

  1. 01 →
    Paste the sequence
    Plain bases or FASTA, any case. Headers, spaces, line numbers and line breaks are removed for you.
  2. 02 →
    Read the numbers
    Length, GC content, base counts and the reverse complement update as you type. Copy the reverse complement with one click.
  3. 03
    Check the ORFs, then share
    Every forward-strand ORF of 30 nt or more is listed, the longest is highlighted and translated, and Share result gives you a link to this analysis.
MethodWHAT THE CODE DOES

How it works: the method

The sequence is cleaned (headers, whitespace and digits removed, upper-cased, U read as T for RNA), then:

GC % = (G + C) / (A + C + G + T) × 100 reverse complement: reverse, then A↔T, C↔G, N→N

Open reading frames are found on the forward strand only. In each of frames +1, +2 and +3 the scan starts at the first ATG and ends at the first in-frame TAA, TAG or TGA; the scan then looks for the next ATG after that stop. ORFs of at least 30 nt, stop codon included, are kept.

The longest ORF is translated with the standard genetic code (NCBI translation table 1). The stop codon is not shown, and a codon containing N becomes X.

Example40 NT · ONE ORF

Worked example

Take this 40 nt sequence:

CCATGGCTAGCAAAGGAGAAGAACTTTTCACTGGATAAGG

It has A 14, C 7, G 11 and T 8, so GC content is (11 + 7) / 40 × 100 = 45.0%. Its reverse complement is:

CCTTATCCAGTGAAAAGTTCTTCTCCTTTGCTAGCCATGG

In frame +3 an ATG starts at position 3 and the first in-frame stop, TAA, ends at 38: one ORF of 36 nt. Translated, it encodes 11 amino acids, MASKGEELFTG.

FIG 3THE FULL WORKSPACE

What the full workspace adds.

Fig 3IN MOREMIND
  • ✓Describe the analysis in plain words and get a Python or R script (e.g. with Biopython) you can read, run and rerun
  • ✓Extend the script to what this peek leaves out: both strands, other genetic codes, multi-sequence FASTA files
  • ✓Charts and diagrams for your report, with code you can edit
  • ✓Verified references for the databases and tools you cite, in your citation style
  • ✓The interpretation stays yours: MoreMind doesn't write your discussion

You still write the argument.

MoreMind handles the mechanics around your work (sources, data, figures and formatting) so your time goes into the thinking. Every result is something you check and decide on.

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FIG 4QUESTIONS

DNA analysis: common questions

How is GC content calculated?

GC content = (G + C) / (A + C + G + T) × 100. Unknown bases (N) are left out of both the top and the bottom, so a run of Ns doesn't lower the figure. The base-composition bar under the result shows each base, N included, as a share of the full length.

How do you find the reverse complement of a DNA sequence?

Reverse the sequence and swap each base for its partner: A with T and C with G (N stays N). The result is the opposite strand read 5′ to 3′. For example, the reverse complement of ATGGCC is GGCCAT.

How are open reading frames found?

In each of the three forward reading frames, the analyser starts at the first ATG and stops at the first in-frame stop codon (TAA, TAG or TGA). Frames of 30 nucleotides or more, stop included, are listed with 1-based start and end positions. ATGs inside an ORF are not listed as separate ORFs, frames without a stop codon are left out, and the reverse strand is not scanned.

Can I paste FASTA or RNA?

Yes. Lines starting with > are dropped, as are spaces, line breaks and numbers, and lower case is converted to upper case. If the sequence has U but no T, it is read as RNA and U becomes T. If you paste several FASTA records they are joined into one sequence. Characters other than A, C, G, T and N (for example IUPAC codes such as R or Y) are reported with their positions.

Can I use these numbers in my report?

Yes, but say how they were computed (for example: GC content over A, C, G and T, excluding N) and check them against your course's preferred tool. For anything you publish, a script you can rerun is better than a web page.

Is my sequence uploaded?

No. The analysis runs in your browser. If you press Share result, the cleaned sequence is written into the link itself (up to 6,000 nt), so anyone who opens the link, and our server, which draws the page and its preview image, sees it.
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