aragorn

aragorn identifies transfer RNA (tRNA) and transfer-messenger RNA (tmRNA) genes, predicts their secondary structures, and reports tmRNA sequences and tag peptides across eubacteria, eukaryotes, archaea, and specific chloroplasts.

Key Features:

• High Sensitivity Detection: Achieves 99% detection sensitivity for tRNA genes as validated on a set of 1290 eubacterial, eukaryotic, and archaeal tRNA sequences.
• Enhanced tmRNA Gene Identification: Uses a modified version of the BRUCE program to identify tmRNA genes, detecting all complete tmRNA sequences present in databases and outperforming the original BRUCE program.
• Comprehensive Output Information: Reports proposed secondary structures for tRNAs; for tmRNA provides the tRNA-domain secondary structure, complete gene sequence, associated tag peptide, and a list of organisms with matching tmRNA peptide tags.
• Detection of Novel Genes: Has identified recently discovered tmRNA genes in the chloroplasts of two green algae species.

Scientific Applications:

• Genomic Annotation: Identification of tRNA and tmRNA genes to support annotation of genomes and genome assemblies.
• Evolutionary Studies: Comparative analysis of tRNA and tmRNA gene conservation and divergence across species.
• Functional Genomics: Characterization of RNA genes to inform studies of gene expression mechanisms, protein synthesis, and regulatory pathways.

Methodology:

Heuristic algorithms predict RNA secondary structures from sequence homology to consensus sequences with tRNA cloverleaf modeling, and tmRNA detection incorporates modifications of the BRUCE program.