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.
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Le but du cours est de fournir un aperçu général de la biologie des cellules et des organismes. Nous en discuterons dans le contexte de la vie des cellules et des organismes, en mettant l'accent sur l
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences), or within a genome (paralogous sequences), or between donor and receptor taxa (xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection. A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time.
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue. When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein.
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
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