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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. solfataricus
sRNA 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
Todd M. Lowe
2000-03-31