{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T02:11:38Z","timestamp":1778897498241,"version":"3.51.4"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The identification of orthologous gene pairs is generally based on sequence similarity. Gene pairs that are mutually \u2018best hits\u2019 between the genomes being compared are asserted to be orthologs. Although this method identifies most orthologous gene pairs with high confidence, it will miss a fraction of them, especially genes in duplicated gene families. In addition, the approach depends heavily on the completeness and quality of gene annotation. When the gene sequences are not correctly represented the approach is unlikely to find the correct ortholog. To overcome these limitations, we have developed an approach to identify orthologous gene pairs using shared chromosomal synteny and the annotation of protein function.<\/jats:p>\n               <jats:p>Results: Assembled mouse and human genomes were used to identify the regions of conserved synteny between these genomes. \u2018Syntenic anchors\u2019 are conserved non-repetitive locations between mouse and human genomes. Using these anchors, we identified blocks of sequences that contain consistently ordered anchors between the two genomes (syntenic blocks). The synteny information has been used to help us identify orthologous gene pairs between mouse and human genomes. The approach combines the mutual selection of the best tBlastX hits between human and mouse transcripts, and inferring gene orthologous relationships based on sharing syntenic anchors, collocating in the same syntenic blocks and sharing the same annotated protein function. Using this approach, we were able to find 19\u2009357 orthologous gene pairs between human and mouse genomes, a 20% increase in the number of orthologs identified by conventional approaches.<\/jats:p>\n               <jats:p>Contact: \u00a0richard.mural@celera.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti045","type":"journal-article","created":{"date-parts":[[2004,10,1]],"date-time":"2004-10-01T00:24:35Z","timestamp":1096590275000},"page":"703-710","source":"Crossref","is-referenced-by-count":44,"title":["Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs"],"prefix":"10.1093","volume":"21","author":[{"given":"Xiangqun H.","family":"Zheng","sequence":"first","affiliation":[{"name":"Assays and Bioinformatics, Celera Genomics Corporation 45 West Gude Drive, Rockville, MD 20850, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fu","family":"Lu","sequence":"additional","affiliation":[{"name":"Assays and Bioinformatics, Celera Genomics Corporation 45 West Gude Drive, Rockville, MD 20850, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen-Yuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Assays and Bioinformatics, Celera Genomics Corporation 45 West Gude Drive, Rockville, MD 20850, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fei","family":"Zhong","sequence":"additional","affiliation":[{"name":"Assays and Bioinformatics, Celera Genomics Corporation 45 West Gude Drive, Rockville, MD 20850, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey","family":"Hoover","sequence":"additional","affiliation":[{"name":"Assays and Bioinformatics, Celera Genomics Corporation 45 West Gude Drive, Rockville, MD 20850, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Mural","sequence":"additional","affiliation":[{"name":"Assays and Bioinformatics, Celera Genomics Corporation 45 West Gude Drive, Rockville, MD 20850, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,9,30]]},"reference":[{"key":"2023013107224230100_B1","unstructured":"Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. 2000The genome sequence of Drosophila melanogaster. 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