fragrep

fragrep detects specific nucleotide pattern fragments occurring in a predefined order within genomic sequences to identify homologs of non-coding RNAs characterized by short conserved elements separated by variable-length poorly conserved regions.

Key Features:

• Ordered fragment detection: Searches for specific nucleotide pattern fragments that occur in a predefined order rather than relying on full-sequence alignment.
• Mismatch tolerance: Allows specification of a tolerance level for mismatches within pattern fragments.
• Intervening-sequence bounds: Supports setting bounds on the length of intervening sequences between pattern fragments.
• Scoring scheme: Implements a statistically well-motivated scoring scheme to rank matches.
• Algorithmic efficiency: Employs an efficient algorithm tailored to detect ordered pattern fragments in genomic sequences.
• ncRNA targets: Enables detection of homologs for ncRNA classes including Y RNAs, vault RNAs, RNase P RNAs, MRP RNAs, and a novel class discovered in Dictyostelium discoideum.
• Alignment complementarity: Addresses limitations of local alignment algorithms such as BLAST for discovering ncRNA homologs.

Scientific Applications:

• ncRNA homolog discovery: Identification of homologs of non-coding RNAs characterized by conserved short elements separated by variable regions.
• Novel ncRNA detection: Discovery and detection of novel ncRNA classes, including the Dictyostelium discoideum class mentioned.
• Complement to local aligners: Complementing BLAST and similar local alignment methods by detecting patterns those methods may miss.
• Genomic context analysis: Investigation of genomic contexts of ncRNAs through ordered fragment pattern detection.

Methodology:

Uses an efficient algorithm to search for ordered nucleotide pattern fragments with user-specified mismatch tolerance and bounds on intervening sequence lengths, and applies a statistically motivated scoring scheme to rank matches.