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RNA STRAND: the RNA secondary structure and statistical analysis database.

Andronescu M, Bereg V, Hoos HH, Condon A - BMC Bioinformatics (2008)

Bottom Line: The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding.We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs.In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada. andrones@cs.ubc.ca

ABSTRACT

Background: The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures.

Results: In this paper we describe RNA STRAND - the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND.

Conclusion: RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

Show MeSH
RNA secondary structure example. Schematic representation of the secondary structure for the RNase P RNA molecule of Methanococcus marapaludis from the RNase P Database; the RNA STRAND ID for this molecule is ASE_00199. Solid grey lines represent the ribose-phosphate backbone. Dotted grey lines represent missing nucleotides. Solid circles mark base pairs. Dashed boxes mark structural features. We define an RNA secondary structure as a set of base pairs [22]. In this work, we consider all C-G, A-U and G-U base pairs as canonical, and all other base pairs as non-canonical. However, we note that from the point of view of the planar edge-to-edge hydrogen bonding interaction [42], there are C-G, A-U and G-U base pairs that do not interact via Watson-Crick edges, and vice-versa [14,42]. Comparative sequence analysis tools do not currently describe bond types. A number of structural motifs can be identified in a secondary structure: A stem is composed of one or more consecutive base pairs. A hairpin loop contains one closing base pair, and all the bases between the paired bases are unpaired. An internal loop is a loop with two closing base pairs, and all bases between them are unpaired. A bulge loop can be seen as a variant of an internal loop in which there are no unpaired bases on one side. A multi-loop is a loop which has at least three closing base pairs; stems emanating from these base pairs are called multi-loop branches. A pseudoknot is a structural motif that involves non-nested, crossing base pairs.
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Figure 1: RNA secondary structure example. Schematic representation of the secondary structure for the RNase P RNA molecule of Methanococcus marapaludis from the RNase P Database; the RNA STRAND ID for this molecule is ASE_00199. Solid grey lines represent the ribose-phosphate backbone. Dotted grey lines represent missing nucleotides. Solid circles mark base pairs. Dashed boxes mark structural features. We define an RNA secondary structure as a set of base pairs [22]. In this work, we consider all C-G, A-U and G-U base pairs as canonical, and all other base pairs as non-canonical. However, we note that from the point of view of the planar edge-to-edge hydrogen bonding interaction [42], there are C-G, A-U and G-U base pairs that do not interact via Watson-Crick edges, and vice-versa [14,42]. Comparative sequence analysis tools do not currently describe bond types. A number of structural motifs can be identified in a secondary structure: A stem is composed of one or more consecutive base pairs. A hairpin loop contains one closing base pair, and all the bases between the paired bases are unpaired. An internal loop is a loop with two closing base pairs, and all bases between them are unpaired. A bulge loop can be seen as a variant of an internal loop in which there are no unpaired bases on one side. A multi-loop is a loop which has at least three closing base pairs; stems emanating from these base pairs are called multi-loop branches. A pseudoknot is a structural motif that involves non-nested, crossing base pairs.

Mentions: The number of solved RNA secondary structures has increased dramatically in the past decade, and several databases are available to search and download specific classes of RNA secondary structures [1-5]. However, for purposes such as improving RNA energy models [6,7], evaluating RNA secondary structure prediction software, obtaining distributions of naturally occuring structural features, or searching RNA molecules with specific motifs, researchers need to easily access a much larger set of known RNA secondary structures, ideally all known RNA secondary structures. RNA STRAND aims to provide this capability, in addition to easy search, analysis and download features. Figure 1 shows an example of an RNA secondary structure and highlights some of its structural features.


RNA STRAND: the RNA secondary structure and statistical analysis database.

Andronescu M, Bereg V, Hoos HH, Condon A - BMC Bioinformatics (2008)

RNA secondary structure example. Schematic representation of the secondary structure for the RNase P RNA molecule of Methanococcus marapaludis from the RNase P Database; the RNA STRAND ID for this molecule is ASE_00199. Solid grey lines represent the ribose-phosphate backbone. Dotted grey lines represent missing nucleotides. Solid circles mark base pairs. Dashed boxes mark structural features. We define an RNA secondary structure as a set of base pairs [22]. In this work, we consider all C-G, A-U and G-U base pairs as canonical, and all other base pairs as non-canonical. However, we note that from the point of view of the planar edge-to-edge hydrogen bonding interaction [42], there are C-G, A-U and G-U base pairs that do not interact via Watson-Crick edges, and vice-versa [14,42]. Comparative sequence analysis tools do not currently describe bond types. A number of structural motifs can be identified in a secondary structure: A stem is composed of one or more consecutive base pairs. A hairpin loop contains one closing base pair, and all the bases between the paired bases are unpaired. An internal loop is a loop with two closing base pairs, and all bases between them are unpaired. A bulge loop can be seen as a variant of an internal loop in which there are no unpaired bases on one side. A multi-loop is a loop which has at least three closing base pairs; stems emanating from these base pairs are called multi-loop branches. A pseudoknot is a structural motif that involves non-nested, crossing base pairs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2536673&req=5

Figure 1: RNA secondary structure example. Schematic representation of the secondary structure for the RNase P RNA molecule of Methanococcus marapaludis from the RNase P Database; the RNA STRAND ID for this molecule is ASE_00199. Solid grey lines represent the ribose-phosphate backbone. Dotted grey lines represent missing nucleotides. Solid circles mark base pairs. Dashed boxes mark structural features. We define an RNA secondary structure as a set of base pairs [22]. In this work, we consider all C-G, A-U and G-U base pairs as canonical, and all other base pairs as non-canonical. However, we note that from the point of view of the planar edge-to-edge hydrogen bonding interaction [42], there are C-G, A-U and G-U base pairs that do not interact via Watson-Crick edges, and vice-versa [14,42]. Comparative sequence analysis tools do not currently describe bond types. A number of structural motifs can be identified in a secondary structure: A stem is composed of one or more consecutive base pairs. A hairpin loop contains one closing base pair, and all the bases between the paired bases are unpaired. An internal loop is a loop with two closing base pairs, and all bases between them are unpaired. A bulge loop can be seen as a variant of an internal loop in which there are no unpaired bases on one side. A multi-loop is a loop which has at least three closing base pairs; stems emanating from these base pairs are called multi-loop branches. A pseudoknot is a structural motif that involves non-nested, crossing base pairs.
Mentions: The number of solved RNA secondary structures has increased dramatically in the past decade, and several databases are available to search and download specific classes of RNA secondary structures [1-5]. However, for purposes such as improving RNA energy models [6,7], evaluating RNA secondary structure prediction software, obtaining distributions of naturally occuring structural features, or searching RNA molecules with specific motifs, researchers need to easily access a much larger set of known RNA secondary structures, ideally all known RNA secondary structures. RNA STRAND aims to provide this capability, in addition to easy search, analysis and download features. Figure 1 shows an example of an RNA secondary structure and highlights some of its structural features.

Bottom Line: The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding.We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs.In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada. andrones@cs.ubc.ca

ABSTRACT

Background: The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures.

Results: In this paper we describe RNA STRAND - the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND.

Conclusion: RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

Show MeSH