are sequence logos better than consensus sequences

ARE SEQUENCE LOGOS BETTER THAN CONSENSUS SEQUENCES ACTIVATOR

ARE SEQUENCE LOGOS BETTER THAN CONSENSUS SEQUENCES ACTIVATOR

( A) CAP (Catabolite Activator Protein, also known as CRP) acts as a transcription promoter by binding at more than 100 sites within the Escherichia coli genome. Additional examples, and the raw data for the example presented here, can be found on the WebLogo examples page ( ). 2001), and in a variety of other contexts. 2002), to analyze splice sites ( Stephens and Schneider 1992 Emmert et al. 1995), and in DNA-binding site motifs ( Robison et al. Sequence logos have also been used to display patterns in the BLOCKS protein sequence database ( Henikoff et al. Protein logos can illuminate patterns of amino acid conservation that are often of structural or functional importance ( Galperin et al. Deviations from this basic pattern can indicate additional features a highly conserved residue in the center of such a pattern may indicate DNA distortion or base flipping ( Schneider 2001) an unexpectedly high-sequence conservation may be due to overlapping binding sites ( Schneider et al. Homodimeric DNA-binding proteins typically display a symmetric double hump in the DNA binding-site logo ( Schneider and Stephens 1990), as shown in the figure. 1) shows how WebLogo can help interpret the sequence-specific binding of the protein CAP to its DNA recognition site ( Schultz et al. As an example, the accompanying figure ( Fig. 1993) to display patterns in sequence conservation, and to assist in discovering and analyzing those patterns. As you probably already know: the proportions of all alternative bases are shown as relative heights of individual letters.Sequence logos were invented by Tom Schneider and Mike Stephens ( Schneider and Stephens 1990 Shaner et al. 68.5% of the time the same base A and in all other case C, G or T with equal frequencies of 10.5%.ī. And, for example, the value of 0.6 would be observed if you had, e.g.

One bit would be obtained if we had, say, just two equally frequent bases. The minimum (0 bits) is when we have no idea about the base. The maximum value (2 bits) would be observed when we always have the same base, because 'actual information' would be zero (there is no need to ask questions - we 'know' the answer anycase). This value defines the height of a stack of letters at each position. Now to estimate the 'the degree of certainty' we simply calculate the information based on the observed frequencies of different residues at this position and subtract it from the theoretical maximum (again: 2 in the case of DNA):Ĭertainty = maximal information possible - actual information Intuition and brief inspection of this formula would bring you the idea, that when the ratios of the residues are biased, we always have less information than for the case of equal frequencies (2 in the case of DNA). When the ratios are not even (or when the number of alternative states is not 2 n), the analogy with the questions becomes much less clear and we have to resort to the very simple formula for Shannon entropy. If we already know, say, that we have just G and A at this position with ratio of 1:1, we can just ask 'is it G?', so we get clearly 1 bit. If the frequencies are distorted, we already have some ideas about the bases when coming to an individual observation. So, when the frequencies are equal we can get 2 bits of information from one observation of a base at this position in a sequence. For example: 'is it Pyrimidine?' If 'yes' we'd ask 'is it 'T'?' Otherwise: 'is it G?'. To 'guess' a base at this position in some sequence we have to ask two binary questions. Let's say we have equal proportions of all four bases at a certain position in a set of DNA sequences. 1 bit of information can be understood as the amount 'knowledge' you get when receiving an answer to one yes/no question. The key parameter in this context is information. Basically, to get the height of the stack of letters for every position one has to calculate the degree of certainty about the residue (= degree of conservation) at this position in the sequences belonging to this class. The starting point is an alignment for the region under investigation.Ī. A very clear description is given in Wikipedia.

Are sequence logos better than consensus sequences