Erpin

Erpin identifies and characterizes RNA structural motifs in sequence databases by converting multiple sequence alignments and secondary structure annotations into single-strand and helical lod-score profiles.

Key Features:

• Input Requirements: Requires a multiple sequence alignment of RNA sequences and corresponding secondary structure annotations as input.
• Profile Construction: Builds single-strand lod-score profiles for linear positions and helical profiles that include 16 lod-scores per position to represent all base-pair combinations.
• Database Search Methodology: Searches databases by simultaneously matching helical profiles and performing dynamic programming alignment of single-strand profiles to detect RNA motifs.
• Iterative Searches: Translates alignments into profiles to enable iterative refinement and enrichment of homologous RNA collections.

Scientific Applications:

• RNA motif identification: Detects known structured RNAs including tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, and miRNAs for studies of RNA structural and functional diversity.

Methodology:

Constructing lod-score profiles from alignments and secondary structure annotations, simultaneous helical-profile matching combined with dynamic programming alignment of single-strand profiles, and iterative profile refinement.