Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 rCAD: A Novel Database Schema for the Comparative Analysis of RNA.

Literature DB >> 24772454

rCAD: A Novel Database Schema for the Comparative Analysis of RNA.

Stuart Ozer, Kishore J Doshi, Weijia Xu, Robin R Gutell.

Abstract

Beyond its direct involvement in protein synthesis with mRNA, tRNA, and rRNA, RNA is now being appreciated for its significance in the overall metabolism and regulation of the cell. Comparative analysis has been very effective in the identification and characterization of RNA molecules, including the accurate prediction of their secondary structure. We are developing an integrative scalable data management and analysis system, the RNA Comparative Analysis Database (rCAD), implemented with SQL Server to support RNA comparative analysis. The platformagnostic database schema of rCAD captures the essential relationships between the different dimensions of information for RNA comparative analysis datasets. The rCAD implementation enables a variety of comparative analysis manipulations with multiple integrated data dimensions for advanced RNA comparative analysis workflows. In this paper, we describe details of the rCAD schema design and illustrate its usefulness with two usage scenarios.

Entities: Chemical Disease Gene Species

Keywords: Bioinformatics; Biological Database; Database Schema; RNA Sequence Analysis

Year: 2011 PMID： 24772454 PMCID： PMC3998205 DOI： 10.1109/eScience.2011.11

Source DB: PubMed Journal: Proc IEEE Int Conf Escience ISSN： 2325-372X

34 in total

1. The structural basis of ribosome activity in peptide bond synthesis.

Authors: P Nissen; J Hansen; N Ban; P B Moore; T A Steitz
Journal: Science Date: 2000-08-11 Impact factor: 47.728

Review 2. The accuracy of ribosomal RNA comparative structure models.

Authors: Robin R Gutell; Jung C Lee; Jamie J Cannone
Journal: Curr Opin Struct Biol Date: 2002-06 Impact factor: 6.809

3. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods.

Authors: R R Gutell; A Power; G Z Hertz; E J Putz; G D Stormo
Journal: Nucleic Acids Res Date: 1992-11-11 Impact factor: 16.971

rCAD: A Novel Database Schema for the Comparative Analysis of RNA.

1. The structural basis of ribosome activity in peptide bond synthesis.

Review 2. The accuracy of ribosomal RNA comparative structure models.

3. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods.

4. STRUCTURE OF A RIBONUCLEIC ACID.

5. Unusual resistance of peptidyl transferase to protein extraction procedures.

6. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

7. Functional modification of 16S ribosomal RNA by kethoxal.

8. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme.

Review 9. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids.

10. GenBank.

1. RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.

2. Structural constraints identified with covariation analysis in ribosomal RNA.

3. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

4. Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems.