How to Create Motif ICM Logo with WebLogo Tools?

Motif ICM Logo is a graphical representation of the ICM (Information Content Matrix). Motif ICM Logo is also referred as Multiple Sequence Alignment Logo, Sequence Conservation Logo, or Sequence Logo.

You can use the WebLogo tool provided by US Berkeley, or threeplusone.com, to create Motif ICM Logo as shown below.

1. Go to weblogo.berkeley.edu Website.

2. Enter the following sequences.

AAGAAT
ATCATA
AAGTAA
AACAAA
ATTAAA
AAGAAT

3. Select "DNA/RNA" as the "Sequence Type", and set "Logo Size per Line" to 18 x 9 cm.

4. Click "Create Logo" button. You see the following sequence logo:

5. Go to weblogo.threeplusone.com Website.

6. Enter the following sequences.

AAGAAT
ATCATA
AAGTAA
AACAAA
ATTAAA
AAGAAT

8. Select "Create WebLogo" You see the following sequence logo:

5. Compare both WebLogos with ICM (Information Content Matrices) from the last tutorial.

[[2.         0.72113611 0.         1.12498132 1.12498132 0.72113611]
 [0.         0.         0.18028403 0.         0.         0.        ]
 [0.         0.         0.27042604 0.         0.         0.        ]
 [0.         0.36056806 0.09014201 0.22499626 0.22499626 0.36056806]]

As you can see that the two WebLogos are showing different matrix values. And both do not match the above ICM. So those WebLogos must be using some different variations.

Actually, the sequence logo for the above ICM should look like the following diagram.

⇒ BioJava - Java Bioinformatics Toolkit

⇐ Motif ICM as Relative Divergence with Bio.motifs

⇑ Biopython for Sequence Motif Analysis

⇑⇑ OBF (Open Bioinformatics Foundation) Tools