Sequence logo

From Christoph's Personal Wiki
Jump to: navigation, search

A sequence logo in bioinformatics is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA or RNA) or amino acids (in protein sequences).

To create sequence logos, related sequences—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 fewer 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 will be scaled according to their frequency. Sequence logos can be used to represent conserved DNA binding sites, where transcription factors bind.


External links



  • Codon Usage Database — data generated from NCBI-GenBank Flat File Release 156.0 [2006-10-15]; 32,775 organisms.
  • AAindex — Amino acid indices and similarity matrices