Provide Input ( MSA( Fasta and ClustalW ), peptide, PSSM)

Select Logo type:

Clustering method:

Specify threshold for clustering (Hobohm1) Threshold (Hobohm1)

Weight on prior (pseudo counts):

Select information content units: Text on y-axis: (the text on the y-axis can be edited at will )
Note: The PSSM of non-weight-matrix inputs will always be calculated in Bits*!     *or Halfbits if chosen.

Available Output Formats. (multi)

Instructions: Simply paste you alignment file in the appropriate box, choose your logo type, clustering method, weight on prior and file format and submit.
Need guided help? See the Instructions>

Advanced Settings

Minimum stack width
Starting position number NOTE! Only for MSA and peptide input.
The x-axis number interval
Select a segment
Set Y-axis range
Show Consensus

This program uses a 20x20-matrix with Blosum62 substitution frequencies to calculate pseudo counts.
It also uses the background frequencies relating to the Blosum62 matrix.
If you prefer a different version, you can use your own by uploading them here. *PLEASE USE THE SAME FORMATS!
Blosum62 matrix
Background frequencies

Need guided help? See the Instructions

Graphical Layout

Stacks Per Line: Lines per page:
Page size [width]x[height]:  
Title (optional):

Graph Layout. (multi)

Amino Acids Colors:
Choose a coloring scheme, or assign the amino acid color manually.
Black is default if the amino acid is unassigned.

Need guided help? See the Instructions

Learn how to make an easy transfer of alignment files from your program or webpage to Seq2Logo

Confidentiality: The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:


For big submissions please keep in mind that the computation time scales exponentially. Eg.
A job of 10000 sequences with a sequence lenght of 38 takes about 20 seconds.
A job of 20000 sequences with a sequence lenght of 38 takes about 80 seconds.
A job of 40000 sequences with a sequence lenght of 38 takes about 6 minuts.
A job of 80000 sequences with a sequence lenght of 38 takes about 24 minuts.
if you submit too large alignments, the job might not finish within the server's time limit of 2 hours. To get results from these large submission you can download a local version of Seq2Logo and run it on your own machine.