A comprehensive review of bioinformatics tools for chromatin loop calling
Li Liu1, Kaiyuan Han2, Huimin Sun3
1Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China.
Briefings in Bioinformatics
|March 7, 2023
Summary
This review surveys bioinformatics tools for calling chromatin loops from 3C-based assays. It categorizes loop-calling algorithms to aid researchers in selecting methods for gene regulation and disease mechanism studies.
Area of Science:
- Genomics and Bioinformatics
- Molecular Biology
- Computational Biology
Background:
- Chromatin loops are crucial for gene regulation and disease mechanisms.
- Chromatin conformation capture (3C) assays identify genome-wide chromatin loops.
- Experimental biases in 3C protocols necessitate specialized bioinformatics tools for accurate loop detection.
Approach:
- This review provides a comprehensive overview of loop-calling algorithms for various 3C-based techniques.
- It discusses experimental biases and denoising algorithms relevant to 3C data.
- Tools are categorized and summarized based on data source and application.
Key Points:
- Accurate chromatin loop identification is vital for understanding gene regulation and disease.
- Various bioinformatics tools exist for calling chromatin loops from 3C data.
- This work systematically reviews and categorizes these tools, addressing experimental biases.
Conclusions:
- This survey aids researchers in selecting appropriate loop-calling methods for downstream analysis.
- It also serves as a valuable resource for developing novel loop-calling algorithms.
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