{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T06:58:03Z","timestamp":1772521083737,"version":"3.50.1"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Identification of functionally equivalent genes in different species is essential to understand the evolution of biological pathways and processes. At the same time, identification of strings of conserved orthologous genes helps identify complex genomic rearrangements across different organisms. Such an insight is particularly useful, for example, in the transfer of experimental results between different experimental systems such as Drosophila and mammals.<\/jats:p>\n               <jats:p>Results: Here, we describe the Encapsulated Gene-by-gene Matching (EGM) approach, a method that employs a graph matching strategy to identify gene orthologs and conserved gene segments. Given a pair of genomes, EGM constructs a global gene match for all genes taking into account gene context and family information. The Hungarian method for identifying the maximum weight matching in bipartite graphs is employed, where the resulting matching reveals one-to-one correspondences between nodes (genes) in a manner that maximizes the gene similarity and context.<\/jats:p>\n               <jats:p>Conclusion: We tested our approach by performing several comparisons including a detailed Human versus Mouse genome mapping. We find that the algorithm is robust and sensitive in detecting orthologs and conserved gene segments. EGM can sensitively detect rearrangements within large and small chromosomal segments. The EGM tool is fully automated and easy to use compared to other more complex methods that also require extensive manual intervention and input.<\/jats:p>\n               <jats:p>Availability: The EGM software, Supplementary information and other tools are available online from http:\/\/vbc.med.monash.edu.au\/\u223ckmahmood\/EGM<\/jats:p>\n               <jats:p>Contacts: \u00a0james.whisstock@monash.edu; geoff.webb@monash.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq339","type":"journal-article","created":{"date-parts":[[2010,6,28]],"date-time":"2010-06-28T00:12:58Z","timestamp":1277683978000},"page":"2076-2084","source":"Crossref","is-referenced-by-count":6,"title":["EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes"],"prefix":"10.1093","volume":"26","author":[{"given":"Khalid","family":"Mahmood","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of Melbourne, Parkville, VIC 3010 and 5Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia"},{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of Melbourne, Parkville, VIC 3010 and 5Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arun S.","family":"Konagurthu","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of Melbourne, Parkville, VIC 3010 and 5Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia"},{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of Melbourne, Parkville, VIC 3010 and 5Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of Melbourne, Parkville, VIC 3010 and 5Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashley M.","family":"Buckle","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of Melbourne, Parkville, VIC 3010 and 5Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geoffrey I.","family":"Webb","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of Melbourne, Parkville, VIC 3010 and 5Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James C.","family":"Whisstock","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of Melbourne, Parkville, VIC 3010 and 5Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia"},{"name":"1 Department of Biochemistry and Molecular Biology, 2ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC 3800, 3National ICT Australia Victoria Research Laboratory, Department of Electrical and Electronic Engineering, 4Department of Computer Science and Software Engineering, University of 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