CRP binding sites in E. coli
Explore an E. coli transcription factor binding motif.
Sequence Logo Generator
FigranMake a sequence logo from aligned sites or a motif matrix and download it for your paper.
- Sites, FASTA or matrix
- Bits or probability
- Free SVG and 300 DPI PNG
49 sequences · FASTA · 22 positions · DNA
Letter height
Positions
Appearance
Sequence logo generator examples
Start with an example and adapt it to your data.
CTCF motif from JASPAR
Plot a position frequency matrix for CTCF.
Splice acceptor sites
Inspect the acceptor window around a splice junction.
LexA SOS boxes, small sample
See how small-sample correction affects 19 sites.
Helix-turn-helix protein motif
View residue conservation in a protein DNA-binding motif.
Signal peptide cleavage sites
Compare residues around human signal peptide cleavage sites.
How to make a sequence logo
Turn aligned sites or a motif matrix into a figure in four steps.
1Add your data
Paste aligned sequences or a matrix, or import a file.
2Choose units
Show information in bits or show letter probabilities.
3Adjust the figure
Set the position numbers and choose colors.
4Download
Download PNG or SVG; use SVG in a Figran multi-panel figure.
Sequence logo input formats
Paste aligned sequences or a motif matrix in any of these formats.
| Format | Example | Common source | How it is read |
|---|---|---|---|
| Aligned sites | ACGT | MEME / HOMER | One aligned sequence per line |
| FASTA | >site1 | FASTA | Headers identify sequences; lowercase letters are retained and converted to uppercase. |
| Clustal / Stockholm | CLUSTAL | Clustal / MAFFT | Sequence blocks are combined by name. |
| JASPAR | A [ 1 2 ] | JASPAR | Counts / Frequencies |
| TRANSFAC | P0 A C G T | TRANSFAC | Counts |
| MEME | ALPHABET= ACGT | MEME | Frequencies |
| Table | A C G T | CSV / TSV | One row per letter or position. |
Read a sequence logo
Each stack is one position; the relative heights show the letters observed there.
- 1Position number
- 2Information scale
- 3Letter height reflects frequency
- 4Stack height reflects information
N = alphabet size; H = Shannon entropy at this position; e(n) = small-sample correction.
Bits or probability
In bits, the total stack height shows information relative to the background. In probability, each nonempty stack sums to one.
References: Schneider & Stephens 1990 · Schneider et al. 1986 · Crooks et al. 2004
Sequence logo generator FAQ
What do bits mean in a sequence logo?
Bits measure the information at a position. With an equal background, DNA has at most 2 bits and protein has at most log₂20, approximately 4.32 bits; letter heights are proportional to frequency.
Why are some positions shorter with few sequences?
Small-sample correction reduces the upward bias caused by estimating information from few observations. It can be turned off and requires counts. For a nonuniform GC background, this tool uses relative entropy without that correction.
Can I make a logo from a position weight matrix?
Yes. Paste a JASPAR, TRANSFAC, MEME or tabular matrix. Counts, frequencies and log₂ odds can be selected; log odds are converted to probabilities using the background.
Should I use bits or probability?
Bits show conservation, while a probability logo makes composition easier to compare at positions with low information.
How is this different from WebLogo?
Both show sequence logos, with different options for calculating information. This tool updates locally and reads JASPAR and MEME matrices; WebLogo offers error bars and more units. Your sequences and matrices stay in your browser.
What colors are used for protein and DNA logos?
The classic DNA scheme colors A green, C blue, G orange and T red. Protein chemistry colors group residues by chemical properties; other schemes and custom colors are available.
How are gaps and ambiguous letters handled?
Gaps and characters outside the selected alphabet are excluded from counts and sample size. For DNA and RNA, this includes N; Sequence Alignment Viewer counts N in its logo, so nucleotide columns containing N can differ. Protein N is counted as asparagine. Occupancy scaling is optional.
Do I need R or Python to make a sequence logo?
No. For reproducible scripts, ggseqlogo and seqLogo for R or Logomaker for Python are other options. You can export a probability matrix here.
Can I show the logo under my alignment?
Yes. Use Sequence Alignment Viewer to export a logo track with the alignment.
Make a sequence logo for your paper
Turn aligned sequences or a motif matrix into a figure.
Make your sequence logo