The significant advances in nucleic acid sequencing technology, in conjunction with the computer revolution, establish the foundation for scientists to utilize computational biology and bioinformatics to begin their efforts to decipher the genes and genomes that code for complex and elaborate machinery and processes inherent to all living organisms. To understand the relationship between nucleotide sequences and the genes and molecular structures they code for, new paradigms and means to process, analyze, organize, and disseminate this information are required. Towards this end, R. Gutell, who initiated these studies in the H. Noller and C. Woese labs, and his laboratory have utilized comparative analysis to determine and/or confirm the structure models for the ribosomal RNAs and the group I and II introns. In the process of these studies, large collections of comparative sequence and structure information were collected, analyzed, organized into various databases, and disseminated on the web through the Comparative RNA Web (CRW) Site and database. The CRW Site and Database contain approximately 14,500 rRNA, group I and II intron, and tRNA sequences, nearly 450 secondary structure and conservation diagrams, alignments for these sequences, nucleotide frequency information, and a database of introns in the rRNAs. All of these sequence and structure entries are organized and available from a relational database management system and have pertinent data associated, including NCBI phylogenetic information for each entry. Detailed nucleotide frequency information and other information are available for our RNA motif and RNA structure-based phylogenetic analysis and publications. Our goals for this proposal are to continue to curate and maintain the current CRW Site, to expand it with new RNA sequences, structures and conservation diagrams, to improve the interface and infrastructure of the CRW Site and database, to develop RNA secondary structure and phylogenetic tree java applets to improve the access to some information associated with RNA structures and phylogenetic trees, and to develop some new programs that will streamline the process of identifying new ribosomal RNA and group I and II intron sequences in GenBank. The information at the CRW Site is utilized by many laboratories studying ribosomal RNA and group I/ll intron structures, RNA structural motifs, RNA folding, and phylogenetic relationships of organisms.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genome Study Section (GNM)
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Rhoades, Marcus M
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University of Texas Austin
Schools of Arts and Sciences
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Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I et al. (2015) R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server. Nucleic Acids Res 43:W15-23
Lee, Jung C; Gutell, Robin R (2014) Helix capping in RNA structure. PLoS One 9:e93664
Gutell, Robin R (2014) Ten lessons with Carl Woese about RNA and comparative analysis. RNA Biol 11:254-72
Shang, Lei; Gardner, David P; Xu, Weijia et al. (2013) Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems. BMC Syst Biol 7 Suppl 4:S13
McFrederick, Quinn S; Cannone, Jamie J; Gutell, Robin R et al. (2013) Specificity between lactobacilli and hymenopteran hosts is the exception rather than the rule. Appl Environ Microbiol 79:1803-12
Feagin, Jean E; Harrell, Maria Isabel; Lee, Jung C et al. (2012) The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. PLoS One 7:e38320
Shang, Lei; Xu, Weijia; Ozer, Stuart et al. (2012) Structural constraints identified with covariation analysis in ribosomal RNA. PLoS One 7:e39383
Lee, Jung C; Gutell, Robin R (2012) A comparison of the crystal structures of eukaryotic and bacterial SSU ribosomal RNAs reveals common structural features in the hypervariable regions. PLoS One 7:e38203
Gardner, David P; Xu, Weijia; Miranker, Daniel P et al. (2012) An Accurate Scalable Template-based Alignment Algorithm. Proceedings (IEEE Int Conf Bioinformatics Biomed) 2012:1-7
Ozer, Stuart; Doshi, Kishore J; Xu, Weijia et al. (2011) rCAD: A Novel Database Schema for the Comparative Analysis of RNA. Proc IEEE Int Conf Escience 2011:15-22

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