Possum

Possum predicts cis-regulatory elements in DNA sequences by scanning with Position Specific Scoring Matrices (PSSMs) and ranking sequence fragments using log-likelihood ratio scores computed with the natural logarithm (base e).

Key Features:

• Position Specific Scoring Matrices (PSSMs): Uses PSSMs to represent cis-element motifs and match them to DNA sequence fragments.
• Log-Likelihood Ratio Scores: Computes log-likelihood ratio scores (natural log, base e) to quantify resemblance between fragments and cis-element matrices.
• High-Scoring Sequence Fragments: Identifies and returns high-scoring fragments as candidate regulatory elements for downstream analysis.

Scientific Applications:

• Transcriptional regulatory mechanism analysis: Detects known transcription factor binding motifs to study regulatory control of gene expression.
• Promoter motif enrichment in co-regulated genes: Identifies overrepresented motifs within promoter sequences of co-regulated gene sets.

Methodology:

Matches sequence fragments to known cis-element matrices using PSSMs and computes log-likelihood ratio scores (natural log, base e) to assess and rank fragments.