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In molecular biology and bioinformatics, the consensus sequence is the calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It represents the results of a multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. Such information is important when considering sequence-dependent enzymes such as RNA polymerase.[1]

Biological significance[edit]

A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several times in the genome and is thought to play the same role in its different locations. For example, many transcription factors recognize particular patterns in the promoters of the genes they regulate. In the same way restriction enzymes usually have palindromic consensus sequences, usually corresponding to the site where they cut the DNA. Transposons act in much the same manner in their identification of target sequences for transposition. Finally splice sites (sequences immediately surrounding the exon-intron boundaries) can also be considered as consensus sequences.

Thus a consensus sequence is a model for a putative DNA binding site: it is obtained by aligning all known examples of a certain recognition site and defined as the idealized sequence that represents the predominant base at each position. All the actual examples shouldn't differ from the consensus by more than a few substitutions, but counting mismatches in this way can lead to inconsistencies.[2]

Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as an up mutation. This kind of mutation will generally make the promoter stronger, and thus the RNA polymerase forms a tighter bind to the DNA it wishes to transcribe and transcription is up-regulated. On the contrary, mutations that destroy conserved nucleotides in the consensus sequence are known as down mutations. These types of mutations down-regulate transcription since RNA polymerase can no longer bind as tightly to the core promoter sequence.

Sequence analysis[edit]

Developing software for pattern recognition is a major topic in genetics, molecular biology, and bioinformatics. Specific sequence motifs can function as regulatory sequences controlling biosynthesis, or as signal sequences that direct a molecule to a specific site within the cell or regulate its maturation. Since the regulatory function of these sequences is important, they are thought to be conserved across long periods of evolution. In some cases, evolutionary relatedness can be estimated by the amount of conservation of these sites.


The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are variable. Consider the following example DNA sequence:


In this notation, A means that an A is always found in that position; [CT] stands for either C or T; N stands for any base; and {A} means any base except A. Y represents any pyrimidine, and R indicates any purine.

In this example, the notation [CT] does not give any indication of the relative frequency of C or T occurring at that position. An alternative method of representing a consensus sequence uses a sequence logo. This is a graphical representation of the consensus sequence, in which the size of a symbol is related to the frequency that a given nucleotide (or amino acid) occurs at a certain position. In sequence logos the more conserved the residue, the larger the symbol for that residue is drawn; the less frequent, the smaller the symbol. Sequence logos can be generated using WebLogo, or using the Gestalt Workbench, a publicly available visualization tool written by Gustavo Glusman at the Institute for Systems Biology.[2]


Bioinformatics tools are able to calculate and visualize consensus sequences. Examples of the tools are JalView and UGENE.

See also[edit]


  1. ^ Pierce, Benjamin A. 2002. Genetics : A Conceptual Approach. 1st ed. New York: W.H. Freeman and Co.
  2. ^ a b Schneider TD (2002). "Consensus Sequence Zen". Appl Bioinformatics 1 (3): 111–119. PMC 1852464. PMID 15130839. 

Original courtesy of Wikipedia: http://en.wikipedia.org/wiki/Consensus_sequence — Please support Wikipedia.
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101 news items

Fred Hutch News Service

Fred Hutch News Service
Mon, 18 May 2015 11:00:00 -0700

The authors then generated a consensus sequence for each group: Cen1-like and Cen13-like. Several sequences also matched unplaced clones from the human genome assembly. These abundant sequences were composed of two a-satellite repeats ...
BMC Blogs Network
Fri, 15 May 2015 05:45:00 -0700

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original ...
Fri, 15 May 2015 06:52:30 -0700

Detailed comparisons revealed particularly high similarity between the HSR2 strain and Halorhabdus utahensis with regards to both the CRISPR-associated proteins and the number of repeats and their consensus sequence (Supplementary Figure S7).
BMC Blogs Network
Fri, 15 May 2015 05:45:00 -0700

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original ...
Tue, 05 May 2015 07:10:16 -0700

... did enable the MinKnow software to run without an Internet connection and enabled Metrichor — the cloud-based basecalling software — to allow the team to upload raw reads even with a slow Internet connection to build the consensus sequence, he said.
Thu, 30 Apr 2015 03:23:06 -0700

Whether or not this vector DNA is still functioning cannot be concluded from our results, as the quantitative PCR method targeted a short consensus sequence only. Notably, MIDGE-Th1 vector DNA did not accumulate in any tissue after repeated injections.
BMC Blogs Network
Sun, 26 Apr 2015 17:39:50 -0700

The consensus sequence for each contig is either based on the highest quality nucleotide in the aligned reads at each position or based on majority rule. The number of reads underlying each consensus base is called “depth” or “coverage”. Coverage ...

BMC Blogs Network (blog)

BMC Blogs Network (blog)
Fri, 17 Apr 2015 03:16:37 -0700

“At the time, I was fortunate that Alan Scott was developing a consensus sequence of human L1 elements just two floors above my lab. What's more, Jef Boeke in Molecular Biology at Hopkins, was an expert who coined the term retrotransposition during ...

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