uORF4u

uORF4u annotates conserved upstream open reading frames (uORFs) to identify conserved leader peptides that may regulate translation and transcription of downstream main ORFs (mORFs) across prokaryotic and eukaryotic genomes, including short ORFs (<100 codons).

Key Features:

• Conservation-Based Prediction: Leverages evolutionary conservation across homologs and genome assemblies to predict functional uORFs.
• Annotation Scope: Annotates conserved uORFs in 5' upstream sequences of a specified protein or sets of homologous proteins and identifies small conserved ORFs within nucleotide sequence sets.
• Output Generation: Produces multiple sequence alignments, sequence logos, and vector-format locus annotations of predicted conserved uORFs.
• Implementation: Implemented in Python3.

Scientific Applications:

• Regulatory uORF Discovery: Identify conserved uORFs encoding leader peptides that can regulate translation and transcription of downstream mORFs in prokaryotes and eukaryotes.
• Comparative Genomics: Assess evolutionary conservation of short ORFs (<100 codons) across homologous proteins and genome assemblies to prioritize candidates for functional studies.
• Small ORF Annotation: Annotate conserved small ORFs within nucleotide sequence collections.
• Candidate Generation without NGS: Provide conservation-based candidate uORFs when transcription- and translation-level next-generation sequencing data are not available.

Methodology:

Leverages evolutionary conservation to identify candidate uORFs by analyzing 5' upstream sequences of specified proteins or homologous protein sets and by scanning nucleotide sequence sets for small conserved ORFs, and outputs multiple sequence alignments, sequence logos, and vector-format locus annotations; implemented in Python3.