tRNAmodpred

tRNAmodpred predicts chemical modifications in transfer RNA (tRNA) sequences by mapping proteome-derived enzyme homologs to RNA modification pathways from the MODOMICS database to infer potential nucleoside modifications.

Key Features:

• Input Requirements: Accepts unmodified tRNA sequences and a corresponding set of protein sequences from a cell's proteome.
• Enzyme Homology Identification: Identifies homologs of known tRNA modification enzymes within the provided proteome.
• Pathway Mapping and Prediction: Maps predicted enzyme activities onto established RNA modification pathways from the MODOMICS database to propose possible modification pathways and specific nucleoside modifications.
• Cross-Species Analysis: Assesses tentative modification statuses by simulating cross-species enzymatic interactions, including predicting eukaryotic tRNA modifications when expressed in bacterial systems.

Scientific Applications:

• Prediction of tRNA modification landscapes: Infers potential modification patterns of tRNAs across different organisms and organelles using proteome and sequence data.
• Functional inference for translation and regulation: Provides hypotheses about how predicted nucleoside modifications may impact protein synthesis and cellular regulation.
• Experimental hypothesis generation: Generates testable predictions about specific tRNA modifications and responsible enzymes to guide experimental validation.
• Cross-species expression analysis: Evaluates how heterologous expression contexts (e.g., eukaryotic tRNAs in bacterial systems) might alter modification patterns based on enzyme presence.

Methodology:

Accepts unmodified tRNA and proteome sequences, identifies homologs of known tRNA modification enzymes, maps predicted enzyme activities onto MODOMICS RNA modification pathways, and integrates sequence analysis with pathway prediction to generate hypotheses about specific nucleoside modifications.