FSFinder

FSFinder predicts programmed ribosomal frameshift sites in genomic and mRNA sequences to identify locations where ribosomal reading-frame shifts enable alternative protein synthesis.

Key Features:

• Frameshift type coverage: Predicts -1 and +1 frameshifts and extends capability to predict frameshifts of other types across sequences.
• Sequence scope: Operates on both genomic and mRNA sequences for frameshift detection.
• Algorithmic detection: Scans sequences and algorithmically identifies shifts in the ribosomal reading frame.
• Viral genomics relevance: Detects programmed ribosomal frameshifting events used by RNA viruses to synthesize fusion proteins from overlapping open reading frames.
• Testing and validation: Has been tested on the genome of Shewanella oneidensis MR-1 for identifying frameshift sites.

Scientific Applications:

• Virology: Studying synthesis of fusion proteins in RNA viruses that use programmed ribosomal frameshifting.
• Genomics and molecular biology: Analyzing genes with overlapping open reading frames across organisms.
• Functional genomics: Investigating novel gene expression mechanisms that rely on programmed ribosomal frameshifting.

Methodology:

Scans genomic and mRNA sequences and uses algorithmic detection to identify potential programmed ribosomal frameshift sites, including -1, +1, and other frameshift types.