RSAT oligo-analysis

RSAT oligo-analysis computes k-mer frequencies and detects statistically over-represented and under-represented oligonucleotides and oligopeptides to identify regulatory motifs and sequence signals such as transcription factor binding sites, restriction sites, RNA termination and polyadenylation signals, and replication origins.

Key Features:

• K-mer frequency computation: Computes and analyzes frequencies of oligonucleotides (k-mers) and oligopeptides across nucleotide and protein sequences.
• Motif discovery: Identifies DNA binding sites for transcription factors by extracting and analyzing upstream regulatory sequences from families of coregulated genes.
• Statistical rigor: Employs an exhaustive statistical approach defining motif significance based on observed frequencies in non-coding sequences from the yeast genome.
• Over-/under-representation detection: Detects motifs that are significantly over-represented or under-represented in input sequence sets.
• Polyadenylation signal analysis: Analyzes oligonucleotide composition downstream of stop codons to identify over-represented words associated with efficiency and positioning, including distributions around ~35 bp after the stop codon.
• Oligopeptide frequency analysis: Computes and analyzes oligopeptide frequencies in protein sequences to reveal sequence patterns.
• Restriction site identification: Detects motifs indicative of restriction sites within bacterial genomes by analyzing motif frequency patterns.
• Comparative genomics and genome-scale pattern matching: Supports comparative genomics and regulatory variation analyses and performs genome-scale pattern matching.
• Data integration: Integrates data from fully sequenced genomes with updates from GenBank for background and comparative analyses.

Scientific Applications:

• Transcription factor binding motif discovery: Identification of putative transcription factor binding sites from coregulated gene upstream regions.
• Restriction site identification: Mapping and detection of restriction motifs in bacterial genomic sequences.
• RNA processing signal detection: Detection of RNA termination and polyadenylation signals by analyzing oligonucleotide composition downstream of stop codons.
• Replication origin analysis: Analysis of oligonucleotide frequency patterns to investigate replication origin sequences.
• Protein sequence analysis: Examination of oligopeptide frequency distributions to study protein sequence features and evolution.

Methodology:

Computes and analyzes k-mer frequencies; performs exhaustive statistical analysis defining motif significance from observed frequencies in non-coding sequences (yeast genome); identifies over- and under-represented motifs; analyzes oligonucleotide composition downstream of stop codons (noting enrichment around 35 bp); extracts and analyzes upstream regulatory sequences from coregulated genes; analyzes oligopeptide frequencies in protein sequences; and performs genome-scale pattern matching and comparative genomics analyses.