RAG: An update to the RNA-As-Graphs resource
- Joseph A Izzo†^{1},
- Namhee Kim†^{1},
- Shereef Elmetwaly^{1} and
- Tamar Schlick^{1, 2}Email author
https://doi.org/10.1186/1471-2105-12-219
© Izzo et al; licensee BioMed Central Ltd. 2011
Received: 30 November 2010
Accepted: 31 May 2011
Published: 31 May 2011
Abstract
Background
In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structure motifs using clustering and build-up approaches. With the increased availability of secondary structures in recent years, we update the RAG resource and provide various improvements for analyzing RNA structures.
Description
Our RAG update includes a new supervised clustering algorithm that can suggest RNA motifs that may be "RNA-like". We use this utility to describe RNA motifs as three classes: existing, RNA-like, and non-RNA-like. This produces 126 tree and 16,658 dual graphs as candidate RNA-like topologies using the supervised clustering algorithm with existing RNAs serving as the training data. A comparison of this clustering approach to an earlier method shows considerable improvements. Additional RAG features include greatly expanded search capabilities, an interface to better utilize the benefits of relational database, and improvements to several of the utilities such as directed/labeled graphs and a subgraph search program.
Conclusions
The RAG updates presented here augment the database's intended function - stimulating the search for novel RNA functionality - by classifying available motifs, suggesting new motifs for design, and allowing for more specific searches for specific topologies. The updated RAG web resource offers users a graph-based tool for exploring available RNA motifs and suggesting new RNAs for design.
Background
The RAG (RNA-As-Graphs) web resource was launched in 2004 to classify and catalogue all possible RNA 2D topologies, including existing and hypothetical motifs http://www.biomath.nyu.edu/rna[1, 2]. RAG's construction was motivated by the increasing importance of RNAs, structurally diverse molecules with significant regulatory roles including protein synthesis, transcriptional regulation and other integral biological functions [3–8]. Many databases have been designed for classifying existing RNAs. These include the NDB (nucleic acid database) [9, 10], Rfam (RNA families with consensus secondary structures) [11, 12], SCOR (structural classifications of RNAs) [13, 14], RNA Strand (secondary structures) [15], and Pseudobase++ (RNAs containing pseudoknots) databases [16, 17].
The current number of RNA tree topologies, divided into existing and yet unreported, the latter subdivided into RNA-like and non-RNA-like by PAM and a supervised clustering algorithm (k-NN) based on existing RNA
V, vertex no. | Existing | RNA-like | Non-RNA-like | Total | ||
---|---|---|---|---|---|---|
PAM | k -NN | PAM | k -NN | |||
2 | 1 | 0 | 0 | 0 | 0 | 1 |
3 | 1 | 0 | 0 | 0 | 0 | 1 |
4 | 2 | 0 | 0 | 0 | 0 | 2 |
5 | 3 | 0 | 0 | 0 | 0 | 3 |
6 | 6 | 0 | 0 | 0 | 0 | 6 |
7 | 9 | 2 | 2 | 0 | 0 | 11 |
8 | 15 | 3 | 5 | 5 | 3 | 23 |
9 | 11 | 22 | 32 | 14 | 4 | 47 |
10 | 10 | 60 | 87 | 36 | 9 | 106 |
Total | 58 | 87 | 126 | 55 | 16 | 200 |
The current number of RNA dual topologies, divided into existing and yet unreported, the latter subdivided into RNA-like and non-RNA-like by PAM and a supervised clustering algorithm (k-NN) based on existing RNA
V, vertex no. | Existing | RNA-like | Non-RNA-like | Total | ||
---|---|---|---|---|---|---|
PAM | k -NN | PAM | k -NN | |||
2 | 3 | 0 | 0 | 0 | 0 | 3 |
3 | 8 | 2 | 0 | 2 | 0 | 8 |
4 | 17 | 8 | 3 | 11 | 10 | 30 |
5 | 18 | 63 | 45 | 36 | 45 | 108 |
6 | 12 | 307 | 239 | 185 | 243 | 494 |
7 | 6 | 1,604 | 1,139 | 783 | 1,243 | 2,388 |
8 | 3 | 8,777 | 5,275 | 3,407 | 6,906 | 12,184 |
9 | 4 | 25,810 | 9,957 | 12,785 | 28,634 | 38,595 |
Total | 71 | 36,571 | 16,658 | 17,209 | 37,081 | 53,810 |
In 2004, we expanded this work on RNA graphs to predict sequences that fold into 10 candidate topologies based on a modular approach using functional submotifs taken from existing structures [32]. That work included a clustering analysis that partitioned all non-existing RNA topologies with 3 and 4 vertices into two classes: "RNA-like" and "non-RNA-like." A recent search of the experimentally verified non-coding RNA databases such as the Rfam database indicated that 5 of the 10 designed candidate topologies now exist in nature. Moreover, they are found in multiple RNA families (see the Discussion section on statistics of current existing topologies).
Since our 2004 work, RNA databases have grown significantly. For example, the RNA family database (Rfam), which displays consensus secondary structures for different families of RNA, had 367 families in 2004, and now contains 1,372 families (database 9.1, December 2008) [11, 12]. The RNA Strand database, which catalogues existing secondary structures from various structure databases including NDB, PDB, and others, now holds 4,666 structures that have been determined from a variety of theoretical and experimental methods such as comparative sequence analysis, NMR data, and X-Ray crystallography [15].
This vast increase in the amount of RNA structural data provides an opportunity to update RAG and to compare our earlier "RNA-like" and "non-RNA-like" classifications to newly discovered RNA. Further, we propose an improved classification of RNA-like and non-RNA-like topologies using a supervised clustering algorithm based on existing RNAs. In addition, we implement various improvements to our RAG web resource such as expanded search tools and a user-friendly interface.
Construction and Content
The original RAG database was designed with the following elements: graphical representations of RNA secondary topologies; Laplacian eigenvalues for quantitative description of RNA graphs; prediction of candidate RNA topologies using a clustering algorithm; and a program for converting secondary structures into RNA tree graphs. In the updated version, we improve upon the database's functionality, apply a supervised clustering algorithm to suggest candidate topologies, and compile the new RNA structures into a user-friendly interface.
RNA graphical representation
- 1)
The 3' and 5' ends of a helical stem constitute a single vertex (•).
- 2)
An RNA stem with more than one complementary base pair is considered an edge (-); complementary base pairs are considered to be AU, GC, and the special case of the GU wobble.
- 3)
A bulge, hairpin, or internal loop is a vertex (•) if there is more than one unpaired nucleotide or non-complementary base pair.
- 4)
An RNA junction is considered to be a vertex (•).
- 1)
The 3' and 5' ends do not have any representation.
- 2)
An RNA stem with more than one complementary base pair is represented as a vertex (•).
- 3)
An edge (-) represents any single strand that has more than one unpaired nucleotide and occurs in segments connecting secondary elements of the 2D structure such as bulges, internal loops, junctions, and stems.
The main advantage of such coarse-grained representations is their reduced space compared to the atomic-level structural space or RNA sequence space. This facilitates addressing many problems in RNA structure and allows cataloging of a finite set of graphs to represent all existing and hypothetical RNA structures.
Topological descriptors of RNA graphs: Laplacian eigenvalues
The graph connectivity is described by a Laplacian matrix constructed from the adjacency and degree matrices of each graph; the full eigenvalue spectrum of the Laplacian matrix can then be computed [1, 32]. The spectrum is useful for differentiating between RNA graphs; the number of zero eigenvalues indicates the number of disconnected elements of the graph and the value of the second smallest eigenvalue (λ_{2}) is a measure of the complexity of the graph (a linear RNA molecule has a smaller λ_{2} value than a branched molecule). Thus, two graphs with differing spectrum are dissimilar, though the converse is not true [32]. Since motif complexity is indicated by the second smallest eigenvalue (λ_{2}) of the Laplacian matrix, the ordering of λ_{2} values for topologies within each vertex number (V) is used in RAG to derive a motif identification number (ID) to distinguish the topological complexities among topologies of a certain vertex number. In RAG, all possible tree graphs up to 10 vertices and dual graphs up to 9 vertices have been enumerated and classified through this system of (V, ID, λ_{2}).
Predicted topologies: RNA-like and non-RNA-like graphs
- 1)
The values from the Laplacian eigenvalue spectrum are transformed through a linear regression into two variables - the intercept (α) and the slope (β). Specifically, we transform the non-zero Laplacian eigenvalues for a V-vertex graph (λ_{2}, λ_{3},..., λ_{V}) into two variables (α, β) by applying the least-squares method regarding the index (2, 3,...,V). The slope β and the intercept α represent the average spacing between eigenvalues and the second eigenvalue (λ_{2}) adjusted by β, respectively.
- 2)
(α, β) is normalized to (α, V*β), because β decreases with the vertex number (V), and thus, V*β can be considered graph-size independent.
- 3)
A distance matrix is created from the variables (α, V*β) corresponding to the pair-wise distance between all RNA graphs.
- 4)
Using the distance matrix in Step 3, PAM is applied to cluster all RNA graphs into two groups.
Briefly, the PAM clustering algorithm for two clusters functions by selecting in turn two representatives (also called medoids) and assigning each member into the closest group among two groups based on the distance matrix. These steps are repeated until the resulting two groups of data points have both maximum dissimilarity between groups and maximum similarity within groups. This method allowed us to classify hypothetical topologies as "RNA-like" or "non-RNA-like"; the former group of topologies is considered more likely to be found in nature.
Cross-validation (CV) results for dual graphs with k-NN (k = 1 to 5) and PAM
Training Set (2010) | Error Rate | |
---|---|---|
Dual graphs (V) | Method | (10-fold CV) [%] |
3-4 | 1-NN | 8 |
(25 existing and 25 missing graphs) | 2-NN | 6 |
3-NN | 8 | |
4-NN | 6 | |
5-NN | 10 | |
PAM | 34 | |
3-5 | 1-NN | 14 |
(43 existing and 43 missing graphs) | 2-NN | 12 |
3-NN | 15 | |
4-NN | 13 | |
5-NN | 14 | |
PAM | 26 | |
3-6 | 1-NN | 13 |
(55 existing and 55 missing graphs) | 2-NN | 13 |
3-NN | 13 | |
4-NN | 13 | |
5-NN | 13 | |
PAM | 26 | |
3-7 | 1-NN | 13 |
(61 existing and 61 missing graphs) | 2-NN | 13 |
3-NN | 13 | |
4-NN | 13 | |
5-NN | 12 | |
PAM | 31 | |
3-8 | 1-NN | 13 |
(64 existing and 64 missing graphs) | 2-NN | 14 |
3-NN | 12 | |
4-NN | 13 | |
5-NN | 13 | |
PAM | 33 | |
3-9 | 1-NN | 13 |
(68 existing and 68 missing graphs) | 2-NN | 13 |
3-NN | 13 | |
4-NN | 13 | |
5-NN | 12 | |
PAM | 36 |
RNA Matrix: a computer program to convert RNA 2D topology to a tree graph
RAG contains the RNA Matrix program to assist structural and functional identification of RNA motifs. It converts a user-supplied secondary structure file (in 'ct' format) into its graphical representation. Essentially, our RNA Matrix program converts a tree secondary structure into an adjacency matrix through the following two steps: (1) the secondary structure file ('ct' file format) is used to define paired (P) and unpaired (U) regions of the RNA sequence. Each U region is associated with a vertex label (1, 2, 3, ...). Regions with the same label belong to the same structural elements (e.g., junctions, bulges). Identifying the U and P regions involves applying the RNA graph rules and also requires careful consideration of possible secondary structure configurations (e.g., where the chain ends occur); (2) the adjacency graph vertices are assigned by following the connecting arrows (from left to right). For dual graphs, the roles of U and P regions are reversed. RNA Matrix calculates the RNA graph's topological characteristics (vertex number, eigenvalues, order of junctions or degree of vertices, etc). Such information directs the user to the corresponding existing (or hypothetical) RNA motif in the database, with links to other RNA sequence, structure (2D and 3D) and function databases. Our RAG update introduces three significant improvements to the RNA Matrix program: first, we have now automated the classification of dual graph as well as tree graph topologies; second, we have extended the limit of 200 nt to 1000 nt and of 10 vertices to any number for tree graphs; third, we added a function to specify the direction for the graphs (5' to 3') and list common subgraphs between two RNA secondary structures. To label vertices, RNA Matrix compares the adjacency matrix of given structures to a set of standard adjacency matrices corresponding to our labeled graphs (visible on the RAG website). Subgraphs are determined by permuting all square submatrices of the structures' adjacency matrices to identify smaller graphs shared by each structure.
Utilities and Discussion
RNA database searches
We determine and classify tree and dual graphs of available secondary structures according to our topological descriptors (Tables 1 and 2). To accomplish this, we use secondary structure information from three comprehensive RNA databases to produce RNA graphs: the Rfam database, which contains the sequence alignments and consensus secondary structures of RNA families; the Pseudobase++ database, a catalogue of pseudoknot structures; and the RNA Strand database, which collects RNA secondary structures from many databases such as the RCSB Protein Databank, Nucleic Acid Database, and others. We use the following criteria for converting database structures to RNA graphs: tree graphs and dual graphs are limited to 10 vertices and 9 vertices, respectively; only RNAs of 200 nt or less are considered. Additionally, only pseudoknot-containing structures are considered by the dual graph representation, because tree graphs cannot represent pseudoknots. The non-pseudoknot structures are represented by both tree and dual graphs.
We consider natural RNAs whose structures are solved by experimental methods, such as NMR or X-ray crystallography or identified by comparative analysis to be existing RNAs. All comparative structures are currently derived from the Pseudobase++, Rfam and RNAStrand databases, while solved structures are from NDB, PDB, and Pseudobase++. The secondary structure prediction by homology modeling exploits multiple RNA sequences to infer accurate conserved secondary structures: the homologous sequences are aligned to determine conserved residues and the common secondary structure is detected by the co-variation of base pairs [11]. In our earlier RAG, we also took account into structures from comparative structure analysis. Indeed, many comparatively analyzed structures have been verified by mutagenesis or chemical probing (see Table S1 in Additional file 1 for the list of Rfam IDs of families whose comparatively analyzed secondary structures are confirmed by mutagenesis or structure probing). Synthetic RNAs are not regarded as existing topologies because they were not found in nature, but designed to have a specific structure or function in vitro. Still, in the RAG resource, we show a list of synthetic RNA structures determined by experimental methods (X-ray crystal structures or NMR), as listed in NDB, PDB or Pseudobase++.
We use the RNA Matrix program (available on our website for single-molecule use) to rapidly deduce tree graph topologies from the available .ct files of RNA Strand and dual graph topologies from the .bpseq secondary structure files of Pseudobase++. We manually determine the topologies for the RNA families of Rfam, if each topology can be represented by a tree graph of 10 vertices or less or a dual graph of 4 vertices or less, because the database does not currently offer secondary structure files. The tree and dual graph topologies are then classified by motif class (existing, RNA-like, or non-RNA-like) and the method used to determine the structure.
Statistics of current existing topologies
In our 2004 work, 200 tree graph topologies were enumerated for motifs up to 10 vertices, and 53,810 dual graph topologies were enumerated for motifs up to 9 vertices (see the last columns of Tables 1 and 2). RNAs corresponding to 24 of the tree graph topologies and 29 of the dual graph topologies were found in structural databases of the time. These topologies were placed into an "existing" classification. The remaining topologies were considered "missing," and subdivided into RNA-like or "non-RNA-like" classifications by predictions made using PAM clustering. Because three of the graphs reported as existing in the 2004 RAG database could not be located currently (they were predicted by Mfold but not confirmed experimentally), the 2004 existing data as reported has been corrected: the set of 24 existing trees have now been reduced to 21 tree graphs. See Table S2 in Additional file 1 for these corrections.
In particular, for the experimental structures, the dual graph has a much higher prediction rate (20 vs. 9, the first bar plot in Figure 3, lower) compared to tree graphs (3 vs. 3, the first bar plot in Figure 3, upper). This is because of the degeneracy of tree representations (i.e., different secondary structures can be represented as same tree topologies) and the higher sample size of solved dual graph structures (527) in contrast to solved tree structures (392) due to the addition of pseudoknot structures from Pseudobase++. However, as shown in the last two bar plot in Figure 3 (for all natural RNAs and all RNAs), though PAM clustering predictions are reasonable, there remains much room for improvement, as we discuss below. Note that there is some overlap among these topologies between different methods of discovery, and therefore the numbers are not additive for all natural RNAs (both experimental and comparative structures) and all RNAs (both natural and synthetic RNAs) as shown in the last two columns of Figure 3.
Assessment of k-NN versus PAM clustering methods
As discussed above, PAM clustering does not employ existing data to weigh the results: PAM selects two representatives and assigns each graph into the closest group among the two groups based on the Euclidian distance matrix of graph descriptors. These steps are repeated until the resulting two groups of graphs minimize the total distance between members in each group as well as maximize the distance between the groups. The members in the group containing more existing graphs are classified as RNA-like topologies.
We now employ instead a supervised k-nearest neighbor (k-NN) algorithm in conjunction with our RAG update. In the k-NN classification, missing motifs are assigned to RNA-like or non-RNA-like topologies based on k closest training data points of existing RNAs; the distances are measured by graph descriptors. The k-NN approach classifies an object according to a majority vote that depends on the object's neighbors: the object is assigned to the class most common among its k nearest neighbors. Thus, no medoids per se are defined as in PAM, and the classification changes as the data set of known RNAs increases. Our reclassification thus yields revised predictions of topologies that are more strongly guided by existing data.
To compare the performance of PAM and supervised clustering in terms of predicting RNA-like topologies, we use a standard statistical procedure, 10-fold cross-validation, in which the data are partitioned into 10 subsets, one of which is used as a training set and the others are used for prediction. Such a procedure is repeated by shuffling the data in various ways, and all predictions are averaged over these rounds. We perform 10-fold cross-validation for k-NN (with k = 1 to 5) and PAM clustering based on different graph sets using the R statistical package [39].
Table 3 shows that the error rate for classification of dual graphs from 3 to 9 vertices is 6-15% for k-NN compared to 26-36% for PAM. We find that k = 3 is a good choice for the former method (see Table 3). The trend is similar for tree graphs (Table S3 in Additional file 1).
Prediction accuracy when partial sets consist of 2004 existing dual graphs and an additional 50% of 2010 data
Training Set | Testing Set | Method | Accuracy (%) |
---|---|---|---|
2004 Existing RNAs | 50% of newly found | 1-NN | 95 |
Plus 50% of New RNAs | RNAs since 2004 | 2-NN | 90 |
(29 existing in 2004, 21 new RNAs, | (21 new existing) | 3-NN | 90 |
and 50 missing dual graphs) | 4-NN | 90 | |
5-NN | 81 | ||
No Training Set (all 71 existing and 53,739 missing graphs) | PAM | 62 |
Reclustering of RNA topologies and comparison of 2004 and current predictions
Our analyses above suggest that the supervised clustering algorithm can better take advantage of newly-confirmed topologies to lower the error rate and increase the accuracy in suggesting candidate RNA-like topologies. Our classification using the supervised k-NN algorithm applied to all existing RNA data is shown in Tables 1 and 2. When compared to predictions in 2004, the number of RNA-like graphs increases slightly for tree graphs (from 111 to 126, the last row in Table 1) and decreases more significantly for dual graphs (from 36,571 to 16,658, the last row in Table 2).
The Updated RAG Database
Searching for functionality and its implications for RNA design
We have applied our RNA graph classification and prediction to RNA structure analysis and design in multiple ways. For example, we have applied our graph classifications to reveal modular RNA architectures by computational analysis of existing pseudoknots and ribosomal RNAs using dual graph isomorphism [40] and discovered motifs corresponding to antibiotics-binding aptamers in genomes by searching our graphs [41]. We have also assessed topological distributions of random pools for in vitro selection based on RAG [42]. Such combinations can be applied to in vitro selection in conjunction with our RAGPOOLS web server http://rubin2.biomath.nyu.edu/ to design new RNA pools with desired topologies [43–45].
Other groups have extended RAG to labeled dual graphs and directed tree graphs, including graph applications to non-coding RNA classification [18–22]. For example, the Brenner group has added labels to our dual graphs, enabling them to construct more detailed models of RNA structures that classify non-coding RNA families [18]. The Asai group has modified our tree graphs to include direction, which has allowed them to predict non-coding RNAs [19]. Heitsch and coworkers used tree graphical representation to analyze the branching degree of entire RNA viral genomes like Hepatitis C (9,400 bases) and, in turn, proposed a new pattern of random tree degrees in graph theory [46, 47]. Knisley and coworkers extended our graph classification by developing more parameters for tree descriptors and providing a quantitative analysis of secondary structure of RNAs [48, 49].
Our RAG update includes various features such as expanded search tools, directed/labeled graph graphs, a subgraph search program, and newly suggested RNA-like topologies. We hope that these improved features will allow users to perform complex queries and apply our resource to RNA design and related problems. In particular, users can use our updated RAG in four significant ways. First, researchers can translate RNA secondary structure into tree and dual graphs without length limitations on our web server http://www.biomath.nyu.edu/rna/analysis/rna_matrix.php. For example, a set of long viral RNAs (~1000 nt) can be translated into tree and dual graphs. Second, neighboring topologies are related to existing ones by size, topology or function and can be explored, which will help to search a family of topologies. Third, new candidate RNA-like topologies can be used for searching genomes. Fourth, RNA graphs can help design new classes of structural RNAs by combining multiple graphs.
Software features
The updated version of RAG includes a program that converts a given secondary structure (in either 'ct' or 'bpseq' format) into a dual graph. Like the version of RNA Matrix for tree graphs released in 2004, users can submit a single secondary structure file for analysis. Using this file, we compute the necessary Laplacian eigenvalues and provide the corresponding dual graph topology, along with labeled vertices and directional information. The adjacency, degree, and Laplacian matrices for the structure are displayed and the common subgraphs between two structures can be evaluated. In addition, a set of secondary structures (up to 1000 ct files) can be submitted to the updated RNA Matrix program for batch processing and the resulting adjacency matrices and graph IDs can be downloaded.
We have changed our back-end database from plain text files into a MYSQL relational database implementation; the relational database tables in RAG have been "normalized" to minimize the redundancy and define relationships between them. By requiring the existence of a related row in another table, we improve the database integrity and make sure that the data entered into the database are valid and consistent. The updated database using a relational database thus allows us to provide different views and more advanced queries for users (e.g., sequence searches by Rfam ID). We plan to update RAG by adding new structures reported from publications or structural databases regularly, so that new information will become accessible on each topology's sub-page. We also invite users to submit their structures to us directly for inclusion in RAG.
We have also modified the front-end code to produce a better user interface; we have changed the format from static pages written in HTML and PHP server-side scripting languages into a rich-Internet compatible interface utilizing Web 2.0 features such as Asynchronous JavaScript and XML (AJAX) techniques.
Conclusions
An improved and updated RAG database has been designed to allow experimentalists and theoreticians to explore currently existing motifs and help suggest novel RNA motifs. The number of available structures has increased, the searching capabilities have been improved, and the web server has a more user-friendly interface and dynamic content.
Because of the translation to a combined PHP and MYSQL interface, future updates of RAG will be accessible via the web resource in real time; each tree and dual graph topology has its own sub-page on the web resource that accesses the database and displays all structures corresponding to that particular topology. Thus, each addition to RAG will be displayed instantaneously on its respective online topology page.
The hypothetical 'RNA-like' topologies predicted by clustering techniques may serve as possible candidates for RNA design. Here we improved the clustering predictions made in 2004 [1, 32] by using a k-NN clustering approach (Tables 1 and 2).
Availability and Requirements
The RAG database, documentation, and software can be accessed on our web server http://www.biomath.nyu.edu/rna. We invite users to experiment and report to us their experiences.
Notes
Declarations
Acknowledgements
This work is supported by the National Science Foundation (DMS-0201160, CCF-0727001) and the National Institute of Health (GM081410).
Authors’ Affiliations
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