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1. Comparative Analysis of RNA (CAR) »General discussion about Comparative Analysis of RNA, Structure models for reference RNA molecules. |
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2. Structure and Evolution (SAE) »Analysis of the Structure and Evolution of Comparative RNA Data. |
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3. RNA Data (DAT) »Comparative RNA Data: alignments, structure model diagrams, information about structures, metadata, and other less analyzed data. |
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4. Supplementary Information for Manuscripts (SIM) »Online appendices to published papers. Currently the Gutell Lab research focuses on five major categories: RNA Structure, Motifs, Folding, rRNA-based Phylogeny, and Lateral Gene Transfer. |
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5. RNA Families (FAM) »Data organized by RNA Families (under development). |
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0. Ancillary Information (AI) »Information related to the Gutell Lab and the Comparative RNA Web Site. |
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Recent Updates
2011-11-23: The CRW Site runs on a new web server (more powerful and larger disk capacity).2011-10-11: Added Pre-Primary Alignments for 16S rRNA to the Sequence Alignment Retrieval page.
2011-10-03: Added the Three-Dimensional Structure presentation (under development). Includes the following pages: 1) Identification of Basepairs and Conformations; 2) Motif: Adenosine Platform; 3) Motif: A-minor; 4) Motif: C Loop; 5) Motif: E Loop; 6) Motif: E-like Loop; 7) Motif: E and E-like Loop; 8) Motif: GAAA Receptor; 9) Motif: H-turn; 10) Motif: K-turn; 11) Motif: Lonepair Triloop; 12) Motif: Tandem G:A Internal Loop; 13) Motif: Tetraloop; 14) Motif: U-turn; 15) Motif: UAA/GAN, UNA/GAN, GA/GAA.
2011-09-02: Added the Appendix to new Statistical Potentials presentation.
2011-09-01: Additions to Structural Statstics: new statistic (Hairpin Comparative/Potential Ratio) and statistics for eight additional RNAs.
2011-08-29: Added the RNA Families section (under development).
2011-08-08: Added RNA2DMap Examples.
Recent CRW Publications (Complete List)
2012 (in press; 04 May 2012): A Comparison of the Crystal Structures of the Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions. PLos One, in press.2012 (in press; 03 May 2012): The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum. PLoS One, in press.
2012 (in press; 10 April 2012): Comparative Analysis of the Higher-Order Structure of RNA. In: Biophysics of RNA Folding ("Biophysics for the Life Sciences" Series). Springer, New York, NY, in press.
2011: R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm. 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), pp. 618-622. [ pm | pmc | DOI ]
2011: RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure. 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), pp. 613-617. [ pm | pmc | DOI ]
2011: rCAD: A Novel Database Schema for the Comparative Analysis of RNA. 7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp. 15-22.
2011: Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure. Journal of Molecular Biology, 413(2):473-483. [ PM | pmc | DOI ]
2011: Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA. PLoS ONE, 6(4):e18768. [ PM | PMC | DOI ]
2010: Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures. The Journal of Physical Chemistry B, 114(42):13497-13506. [ PM | pmc | DOI ]
2010: Fragmentation of the Large Subunit Ribosomal RNA Gene in Oyster Mitochondrial Genomes. BMC Genomics, 11(1):485. [ PM | PMC | DOI ]
2010: Placement of attine ant-associated Pseudonocardia in a global phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 98(2):195-212. [ PM | PMC | DOI ]
