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Consensus Alignment

The comparison of a structure against a set of similar structures makes it possible to highlight on the one hand the characteristic of the structure of interest and on the other hand the common characteristics and the differences with whole of the other structures. The rendering of consensus alignment is a conveniant way to represent and analyze these various points. For instance, the image of figure 1 corresponds to the comparison of "|AB047642.1/9329-9379|Hepatitis C virus|HepC_CRE" against the whole of the members of its family available in RFam 8.11 by using the rendering tool of RNAStrAT SSRE2.

This image is a graphic illustration of the statistical data presented in You S, Stump DD, Branch AD, Rice CM. A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J Virol. 2004 Feb;78(3):1352-66.3 (figure 2). One can see the perfectly preserved parts where the bases are circled in only one color and parts preserved overall well where the circles are made up mainly of one color. The parts prone to changes are those where the circles are composed of several colors indicating the bases towards which the changes take place. The sites of insertions or possible suppressions are notified by rates of insertions on the junctions between two bases and of the more or less intense crosses on the sometimes removed bases. The speficifities of the structure of interest can be easily pointed out: a base of a color surrounded by a circle of different colors indicates that the nature of this base is specific to this structure. In the same way, if the base is clearly barred it indicates that it is present only in this structure. A number located on the junction between two bases to which the value is close to the number of structures of the dataset suggests that there is only on this structure that an intermediate base was removed (nb: the number indicated being an average, it will be necessary to check all the structures to confirm that indication).

Hepatitis C virus comparison
Figure 1: consensus alignment of "|AB047642.1/9329-9379|Hepatitis C virus|HepC_CRE" with its family members (348) using RNAStrAT server.
Hepatitis C virus figure 4
Figure 2: Copy of figure 4 of You S, Stump DD, Branch AD, Rice CM. A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J Virol. 2004 Feb;78(3):1352-66.
Analysis of conserved nucleotides and covariant base pairs in 5BSL3.2.(...)


Source Data:

Query Structure:


HepC_CRE Family Structures of Hepatitis C Virus:


  1. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. RFam: an RNA family database, Nucleic Acids Research, 2003, 31, 1, 439-441.
  2. Guignon V, Chauve C, Hamel S, RNAStrAT - Secondary Structure Rendering Engine (RSSSR Engine), published by the authors at http://www-lbit.iro.umontreal.ca/rnastrat/?p=tools&p2=render, 2007.
  3. You S, Stump DD, Branch AD, Rice CM. A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J Virol. 2004 Feb;78(3):1352-66.(Pubmed)