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RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures.

Popenda M, Blazewicz M, Szachniuk M, Adamiak RW - Nucleic Acids Res. (2007)

Bottom Line: The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a 'dot-bracket' notation.Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters.The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.

ABSTRACT
The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a 'dot-bracket' notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the 'dot-bracket' notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs. Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters. The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs. The RNA FRABASE is automatically, monthly updated and is freely accessible at http://rnafrabase.ibch.poznan.pl (mirror at http://cerber.cs.put.poznan.pl/rnadb).

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The RNA FRABASE flowchart.
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Figure 2: The RNA FRABASE flowchart.

Mentions: The flowchart representation of RNA FRABASE showing the relations between all of its components is presented in Figure 2. The RNA FRABASE runs in SUSE Linux environment. It has been developed as the relational database in PostgreSQL. The search engine is served by the Apache http daemon along with the PHP scripts. The interface component consists of the web pages designed and implemented in HTML. The assistant programs have been encoded in AWK and PHP. The RNA FRABASE has been tested on Windows and Unix/Linux platforms. It can be operated through many web browsers, like Mozilla, Firefox, Internet Explorer and Opera. The service is hosted and maintained by the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.Figure 2.


RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures.

Popenda M, Blazewicz M, Szachniuk M, Adamiak RW - Nucleic Acids Res. (2007)

The RNA FRABASE flowchart.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238875&req=5

Figure 2: The RNA FRABASE flowchart.
Mentions: The flowchart representation of RNA FRABASE showing the relations between all of its components is presented in Figure 2. The RNA FRABASE runs in SUSE Linux environment. It has been developed as the relational database in PostgreSQL. The search engine is served by the Apache http daemon along with the PHP scripts. The interface component consists of the web pages designed and implemented in HTML. The assistant programs have been encoded in AWK and PHP. The RNA FRABASE has been tested on Windows and Unix/Linux platforms. It can be operated through many web browsers, like Mozilla, Firefox, Internet Explorer and Opera. The service is hosted and maintained by the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.Figure 2.

Bottom Line: The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a 'dot-bracket' notation.Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters.The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.

ABSTRACT
The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a 'dot-bracket' notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the 'dot-bracket' notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs. Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters. The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs. The RNA FRABASE is automatically, monthly updated and is freely accessible at http://rnafrabase.ibch.poznan.pl (mirror at http://cerber.cs.put.poznan.pl/rnadb).

Show MeSH
Related in: MedlinePlus