Sequence logo
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[edit | edit source]
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[edit | edit source]
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[edit | edit source]
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[edit | edit source]
Several software tools are available for generating sequence logos, including:
Related Concepts[edit | edit source]
See Also[edit | edit source]
References[edit | edit source]
External Links[edit | edit source]
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Contributors: Prab R. Tumpati, MD
