CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments - PubMed (original) (raw)

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments

Eckart Bindewald et al. Nucleic Acids Res. 2006.

Abstract

We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual information of two alignment positions as well as the position-specific fraction of gaps. The nucleotide composition of both single columns and column pairs is visualized with the help of color-coded 3D bars labeled with letters. The server generates both VRML and JVX output that can be viewed with a VRML viewer or the JavaView applet, respectively. We show that combining these different features of an alignment into one 3D representation is helpful in identifying correlations between bases and potential RNA and DNA base pairs. Significant known correlations between the tRNA 3' anticodon cardinal nucleotide and the extended anticodon were observed, as were correlations within the amino acid acceptor stem and between the cardinal nucleotide and the acceptor stem. The online server can be accessed using the URL http://correlogo.abcc.ncifcrf.gov.

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Figures

Figure 1

Figure 1

An annotated screenshot of the graphics output corresponding to an alignment of 1114 tRNA sequences showing 2D and 3D sequence logos. The 3D arrows point from the 5′ end to the 3′ end of the alignment. The labels ‘a’ to ‘e’ correspond to the base pairs G15:C48, G19:C56, C13:G46, G22:G46 and G18:G19, respectively. The black cubes correspond to base pairs in a reference consensus secondary structure. Only stacks corresponding to mutual information values Mij ≥ 0.01 bits and Mij ≥ 2 SDs are shown. The sequences correspond to the ‘seed’ alignment of RFAM entry RF00005, RFAM database version 7 (20,21). The consensus secondary structure provided by RFAM originated from (36).

Figure 2

Figure 2

tRNA consensus secondary structure according to RFAM entry RF00005 (20,21,36) mapped onto the sequence of yeast (S.cerevisiae) Phe-tRNA (GenBank accession no. K01553.1). The correlations a, b, c, d and e (compare Figures 1 and 2) are indicated by dashed lines.

Figure 3

Figure 3

A 3D sequence logo of the loop E region of 5S ribosomal RNA [from RFAM entry RF00001 (20,21,35)]. Individual bars corresponding to base pairs are labeled in this view. The gray bars depict with their height the standard deviation of the estimated information in the 2D logos and the mutual information in the 3D logos. Stacks corresponding to mutual information values of <0.5 bits are not shown. The labels a–c correspond to pairs of positions that are not Watson–Crick base pairs and have a mutual information >0.5 bits.

Figure 4

Figure 4

A consensus secondary structure of the loop E region of 5S ribosomal RNA derived from the 3D sequence logo is shown in Figure 3. The consensus structure is mapped onto the loop E region of E.coli 5S rRNA sequence (AB03926.1/6056-6092). The labels a–c correspond to pairs of positions that are not Watson–Crick base pairs and have a mutual information >0.5 bits.

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