CHSMiner: a GUI tool to identify chromosomal homologous segments

doi:10.1186/1748-7188-4-2

Algorithms for Molecular Biology

Volume 4

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Software article

CHSMiner: a GUI tool to identify chromosomal homologous segments

Zhen Wang¹^,2 , Guohui Ding¹^,2 , Zhonghao Yu³ , Lei Liu¹^,4 and Yixue Li¹^,3^,4

¹Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, PR China

²Graduate School of the Chinese Academy of Sciences, Shanghai 200031, PR China

³College of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China

⁴Shanghai Centre for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, PR China

author email corresponding author email

Algorithms for Molecular Biology 2009, 4:2doi:10.1186/1748-7188-4-2


Published:	15 January 2009

Abstract

Background

The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs.

Results

Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source.

Conclusion

CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes.