Sequence logo

In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). A sequence logo is created from a collection of aligned sequences and depicts the consensus sequence and diversity of the sequences. Sequence logos are frequently used to depict sequence characteristics such as protein-binding sites in DNA or functional units in proteins. A sequence logo consists of a stack of letters at each position. The relative sizes of the letters indicate their frequency in the sequences. The total height of the letters depicts the information content of the position, in bits. To create sequence logos, related DNA, RNA or protein sequences, or DNA sequences that have common conserved binding sites, are aligned so that the most conserved parts create good alignments. A sequence logo can then be created from the conserved multiple sequence alignment. The sequence logo will show how well residues are conserved at each position: the higher the number of residues, the higher the letters will be, because the better the conservation is at that position. Different residues at the same position are scaled according to their frequency. The height of the entire stack of residues is the information measured in bits. Sequence logos can be used to represent conserved DNA binding sites, where transcription factors bind. The information content (y-axis) of position is given by: for amino acids, for nucleic acids, where is the uncertainty (sometimes called the Shannon entropy) of position Here, is the relative frequency of base or amino acid at position , and is the small-sample correction for an alignment of letters. The height of letter in column is given by The approximation for the small-sample correction, , is given by: where is 4 for nucleotides, 20 for amino acids, and is the number of sequences in the alignment. A consensus logo is a simplified variation of a sequence logo that can be embedded in text format.