smORFer

smORFer detects small open reading frames (smORFs) encoding proteins of 50 amino acids or fewer in prokaryotic genomes by integrating genome sequencing, ribosome profiling (Ribo-Seq), and translation initiation stalling sequencing (TIS-seq) to empirically annotate translated smORFs.

Key Features:

• smORF detection: Identifies smORFs encoding proteins of 50 amino acids or fewer in prokaryotic genomes.
• Data integration: Integrates genome sequencing, ribosome profiling (Ribo-Seq), and translation initiation stalling sequencing (TIS-seq).
• RPF-based mapping: Uses ribosome-protected fragments (RPFs) from Ribo-Seq to precisely locate actively translated ORFs on mRNA.
• Initiation site identification: Leverages TIS-seq, which blocks ribosomes at the start codon, to sequence protected fragments and identify translation initiation sites.
• Sequence and translation pattern analysis: Considers structural features of genetic sequences and in-frame translation patterns to evaluate candidate smORFs.
• Fourier transform scoring: Applies a Fourier transform to convert sequence and translation parameters into a measurable score for selecting putative smORFs.
• Prokaryotic genome challenges addressed: Accounts for polycistronic messages, overlapping ORFs, leaderless translation, and non-canonical initiation sites.

Scientific Applications:

• Coding sequence annotation: Empirical annotation of coding sequences, specifically smORFs, in prokaryotic genomes.
• Translation initiation mapping: Precise identification of translation initiation sites using TIS-seq and Ribo-Seq data.
• Discovery of non-canonical translation: Detection of leaderless translation and non-canonical initiation events in prokaryotes.
• Functional small protein studies: Enabling discovery and study of small proteins implicated in physiological processes.

Methodology:

Integrates genome sequencing, Ribo-Seq (RPF mapping), and TIS-seq (ribosome stalling at start codons); analyzes structural sequence features and in-frame translation patterns; and employs a Fourier transform to convert parameters into a score for selecting putative smORFs.