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The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. ... Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. ... Graphical display of CHS Conclusion CHSMiner is designed to identify chromosomal homologous segments based on gene content alone, which enables it to discover highly degenerated homology. ...doi:10.1186/1748-7188-4-2 pmid:19146671 pmcid:PMC2647922 fatcat:noa4yvhugzboxltzkqejffcvoy