EpiAlignment

EpiAlignment aligns genomic regions by integrating DNA sequence and ChIP-seq epigenomic profiles from two species to support comparative epigenomic analysis.

Key Features:

• Dual Data Integration: Accepts DNA sequences and ChIP-seq–derived epigenomic profiles from two species for combined sequence and epigenome comparison.
• Semi-Global Alignment Output: Uses computed EpiAlignment scores to generate best semi-global alignments between input datasets, combining sequence alignment and epigenome similarity.
• High-Performance Computing: Can automatically initiate up to 140 computing threads based on the size of input data to accelerate computations.
• Pre-Compiled Datasets: Provides pre-compiled human and mouse epigenomic datasets matched across cell types and tissues sourced from Roadmap Epigenomics and ENCODE.

Scientific Applications:

• Comparative epigenomics: Facilitates cross-species comparison of genomic regions by integrating sequence and epigenomic information.
• Regulatory element conservation: Aids identification of conserved regulatory elements and epigenomic signatures underlying gene regulation across species.

Methodology:

EpiAlignment applies a dynamic programming algorithm to compute EpiAlignment scores that integrate DNA sequence similarity and epigenome congruence from ChIP-seq profiles and uses those scores to produce best semi-global alignments; computations may utilize up to 140 threads.