FMSClusterFinder

FMSClusterFinder detects clusters of sequential motifs in DNA and RNA sequences to identify cooperative functional elements involved in gene regulation and genomic structure.

Key Features:

• Cluster Detection: Identifies clusters of sequential blocks or motifs that may vary in sequence and inter-block distance within subject sequences.
• Sequence Scope: Operates on both DNA and RNA sequences.
• User-Defined Parameters: Supports specification of motif similarity levels, a minimum number of blocks per query cluster, selection between degenerate or standard sequence types, and inclusion of one or multiple alternative sequences for each block.

Scientific Applications:

• Gene Regulation Analysis: Detects cooperative motif clusters that can elucidate mechanisms of gene expression regulation.
• Functional Genomic Element Characterization: Identifies functional groups and their structural roles within genomic contexts.

Methodology:

Uses an algorithm that detects clusters of sequential motifs while accommodating variation in motif sequence and inter-block distances.