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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
Database schema. Construction of RNA STRAND, from data collection to data presentation via dynamic web pages.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 2: Database schema. Construction of RNA STRAND, from data collection to data presentation via dynamic web pages.

Mentions: Figure 2 describes the four main modules that comprise RNA STRAND. To create the database, we first collected the data from various external sources, then we processed the data and prepared it for a MySQL relational database. Next, we installed and populated the database, and finally we prepared dynamic web pages that interact with the database. In what follows we describe in detail the construction and content of each module.


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

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

Database schema. Construction of RNA STRAND, from data collection to data presentation via dynamic web pages.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Database schema. Construction of RNA STRAND, from data collection to data presentation via dynamic web pages.
Mentions: Figure 2 describes the four main modules that comprise RNA STRAND. To create the database, we first collected the data from various external sources, then we processed the data and prepared it for a MySQL relational database. Next, we installed and populated the database, and finally we prepared dynamic web pages that interact with the database. In what follows we describe in detail the construction and content of each module.

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