Contents

• Contents
• List of Tables
• List of Figures
• Introduction
  • Genome Annotation and Gene Prediction
  • Computational Detection of RNA genes
  • Application of New Tools for Biological Research
  • The Small Nucleolar RNAs
    • Common Characteristics
    • Phylogenetic Range
    • Associated Proteins
    • Biological Functions
    • Methylation Guide snoRNAs
  • Ribosomal RNA Modifications
• tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
  • Abstract
  • Introduction
  • Methods
    • tRNAscan 1.4
    • Implementation of EufindtRNA
    • Selenocysteine tRNA Identification
    • Databases Tested
    • ``Random'' Sequence Data
    • Implementation & Online Analysis
  • Results
    • Sensitivity
    • Genome Analysis
    • Selectivity
    • Selenocysteine tRNA Detection
    • Intron Detection
    • Performance on Mitochondrial tRNAs
  • Discussion
    • Speed, Sensitivity, and Selectivity
    • tRNA False Positives & Pseudogenes
    • Conclusion
• Analysis of the Genomic Complement of C. elegans tRNAs
  • Introduction
  • Methods
  • Results and Discussion
    • Intron Occurrence and Genome Distribution
    • C. elegans Follows Wobble Predictions
    • tRNA Gene Redundancy and Codon Frequency
    • tRNA Pseudogenes
    • A tRNA-derived SINE
  • Conclusions
• A Computational Screen for Methylation Guide snoRNAs in Yeast
  • Abstract
  • Introduction
  • Experimental Procedures
    • snoRNA Search Algorithm and Model Scoring
    • snoRNA Gene Disruptions
    • Mapping of rRNA Ribose Methylations by Primer Extension
    • Verification of snoRNA Transcription and 5'-ends
  • Results
    • Computer Search Algorithm and Probabilistic snoRNA Model
    • snoRNAs Assigned to 39 of 42 Known Ribose Methyl Sites
    • snoRNAs Assigned to 12 of 13 Previously Unmapped Ribose Methyl Sites
    • Expression and 5' ends of New Yeast snoRNAs Verified
    • snR70 Identified by Comparative Genomics
  • Discussion
    • snoRNAs Assigned to 51 of 55 Total Ribose Methyl Sites
    • A Nearly Complete Set of Methylation Guide snoRNAs in Yeast
    • Multiple Methylations Guided by Single snoRNAs
    • Methylation Guide snoRNA Consensus Structure
    • Genomic Organization of the snoRNA Gene Family
    • Implications for Genome Sequence Analysis
  • Acknowledgments
  • Data availability
• Small Nucleolar RNAs in Archaeal Genomes
  • Abstract
  • Introduction
  • S. acidocaldarius has aFIB, aNOP and C/D box sRNAs
  • Methylation sites in Ribosomal RNA
  • Identification of an S. solfataricussRNA Homolog
  • A Computational Screen for Additional Archaeal sRNAs
  • sRNAs in Both Main Branches of the Archaea
  • Pyrococcal sRNA families
  • Pyrococcus sRNA Genome Distribution
  • Conserved Sites of Methylation in 16S and 23S rRNA
  • Evolutionary Origin and Divergence of C/D box sRNAs
  • rRNA Methylation and Hyperthermophily
  • Conclusions
• Bibliography