EpiAlign

EpiAlign is a local alignment algorithm for comparing and identifying common patterns in multi-track epigenomic signals. Unlike alignment tools focusing on nucleotide or protein sequences, EpiAlign explicitly addresses the need to compare epigenomic data.

The algorithm utilizes dynamic programming and incorporates varying lengths and frequencies of chromatin states to detect locally aligned chromatin regions. EpiAlign has been shown to be effective in extracting recurrent chromatin state patterns within a single epigenome, many of which exhibit cell-type-specific characteristics.

It can also identify common chromatin state patterns across multiple epigenomes, making it a valuable tool for grouping and distinguishing epigenomic samples based on genome-wide and local chromatin state patterns. EpiAlign fills a crucial gap in the analysis of epigenomic data and facilitates the study of epigenetic modifications and their relationships with chromatin structures and gene expression.