Sequence logo

KozakConsensus

LexA gram positive bacteria sequence logo

LexA gram positive bacteria consensus logo

PF03377

Sequence logo

A sequence logo is a graphical representation used in bioinformatics to illustrate the conservation of nucleotide or amino acid sequences. Sequence logos are commonly used to display the results of multiple sequence alignments and to highlight regions of high conservation and variability within a set of sequences.

History

The concept of sequence logos was first introduced by Thomas D. Schneider and R. Michael Stephens in 1990. They developed this method to provide a more informative visualization of sequence alignments compared to traditional consensus sequences.

Construction

A sequence logo is constructed by stacking letters representing nucleotides or amino acids at each position in the sequence. The height of each letter is proportional to its frequency at that position, and the overall height of the stack indicates the information content at that position, measured in bits. The information content is calculated using Shannon entropy.

Applications

Sequence logos are widely used in various fields of molecular biology and genomics, including:

• Identifying promoter regions in DNA sequences.
• Analyzing protein-DNA interactions.
• Studying protein-protein interactions.
• Investigating RNA secondary structures.

Software Tools

Several software tools are available for generating sequence logos, including:

• WebLogo
• Seq2Logo
• LogoMaker

Related Concepts

• Consensus sequence
• Motif (biochemistry)
• Position weight matrix
• Sequence alignment

See Also

• Bioinformatics
• Genomics
• Molecular biology
• Shannon entropy