enhancerHomologSearch

enhancerHomologSearch identifies putative mammalian orthologs to given enhancers by retrieving ENCODE H3K4me1 peak data and searching for homolog regions across species.

Key Features:

• ENCODE Data Retrieval: The tool retrieves ENCODE data of enhancer regions via H3K4me1 peaks.
• Homolog Region Search: The tool searches for homolog regions for given sequences.
• Distance Filtering: Candidates of enhancer homolog regions can be filtered by distance to target TSS.
• Cross-Species Alignment: The top candidates from human and mouse are aligned to each other.
• Multiple Alignment Export: Results are exported as multiple alignments with the given enhancer.

Scientific Applications:

• Enhancer Ortholog Identification: Identification of putative mammalian orthologs to given enhancers.
• Comparative Genomics: Cross-species comparison of enhancer regions between human and mouse.

Methodology:

The tool retrieves ENCODE enhancer region data via H3K4me1 peaks, searches for homolog regions for given sequences, filters candidates by distance to target TSS, aligns top candidates from human and mouse to each other, and exports results as multiple alignments with the given enhancer.