{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T10:45:29Z","timestamp":1759401929667},"publisher-location":"Berlin, Heidelberg","reference-count":25,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540289326"},{"type":"electronic","value":"9783540318149"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005]]},"DOI":"10.1007\/11554714_6","type":"book-chapter","created":{"date-parts":[[2005,12,15]],"date-time":"2005-12-15T05:47:00Z","timestamp":1134625620000},"page":"61-72","source":"Crossref","is-referenced-by-count":37,"title":["OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements"],"prefix":"10.1007","author":[{"given":"Christophe","family":"Dessimoz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gina","family":"Cannarozzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuel","family":"Gil","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Margadant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Roth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrian","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gaston H.","family":"Gonnet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"6_CR1","doi-asserted-by":"publisher","first-page":"99","DOI":"10.2307\/2412448","volume":"19","author":"W.M. Fitch","year":"1970","unstructured":"Fitch, W.M.: Distinguishing homologous from analogous proteins. Syst. Zool.\u00a019, 99\u2013113 (1970)","journal-title":"Syst. Zool."},{"key":"6_CR2","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1186\/gb-2001-2-4-comment1005","volume":"2","author":"E.V. Koonin","year":"2001","unstructured":"Koonin, E.V.: An apology for orthologs - or brave new memes. Genome. Biol.\u00a02, COMMENT1005 (2001)","journal-title":"Genome. Biol."},{"key":"6_CR3","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1126\/science.278.5338.631","volume":"278","author":"R.L. Tatusov","year":"1997","unstructured":"Tatusov, R.L., Koonin, E.V., Lipman, D.J.: A genomic perspective on protein families. Science\u00a0278, 631\u2013637 (1997)","journal-title":"Science"},{"key":"6_CR4","doi-asserted-by":"crossref","unstructured":"Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Rao, B.S., Smirnov, S., Sverdlov, A.V., Vasudevan, S., Wolf, Y.I., Yin, J.J., Natale, D.A.: The cog database: an updated version includes eukaryotes. BMC Bioinformatics\u00a04 (2003), \n                  \n                    http:\/\/www.biomedcentral.com\/1471\u20132105\/4\/41","DOI":"10.1186\/1471-2105-4-41"},{"key":"6_CR5","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"S.F. Altschul","year":"1997","unstructured":"Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res.\u00a025, 3389\u20133402 (1997)","journal-title":"Nucleic Acids Res"},{"key":"6_CR6","doi-asserted-by":"publisher","first-page":"4029","DOI":"10.1093\/nar\/28.20.4029","volume":"28","author":"W. Fujibuchi","year":"2000","unstructured":"Fujibuchi, W., Ogata, H., Matsuda, H., Kanehisa, M.: Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. Nucleic Acids Res.\u00a028, 4029\u20134036 (2000)","journal-title":"Nucleic Acids Res."},{"key":"6_CR7","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1093\/nar\/gkh063","volume":"32","author":"M. Kanehisa","year":"2004","unstructured":"Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: The KEGG resource for deciphering the genome. Nucleic Acids Res.\u00a032, 277\u2013280 (2004)","journal-title":"Nucleic Acids Res."},{"key":"6_CR8","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"T.F. Smith","year":"1981","unstructured":"Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol.\u00a0147, 195\u2013197 (1981)","journal-title":"J. Mol. Biol."},{"key":"6_CR9","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1006\/jmbi.2000.5197","volume":"314","author":"M. Remm","year":"2001","unstructured":"Remm, M., Storm, C., Sonnhammer, E.: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol.\u00a0314, 1041\u20131052 (2001)","journal-title":"J. Mol. Biol."},{"key":"6_CR10","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1101\/gr.1224503","volume":"13","author":"L. Li","year":"2003","unstructured":"Li, L., Stoeckert, C.J.J., Roos, D.S.: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res.\u00a013, 2178\u20132189 (2003)","journal-title":"Genome Res."},{"key":"6_CR11","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1101\/gr.212002","volume":"12","author":"Y. Lee","year":"2002","unstructured":"Lee, Y., Sultana, R., Pertea, G., Cho, J., Karamycheva, S., Tsai, J., Parvizi, B., Cheung, F., Antonescu, V., White, J., Holt, I., Liang, F., Quackenbush, J.: Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome. Res.\u00a012, 493\u2013502 (2002)","journal-title":"Genome. Res."},{"key":"6_CR12","doi-asserted-by":"publisher","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","volume":"96","author":"M. Pellegrini","year":"1999","unstructured":"Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D., Yeates, T.O.: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U. S. A.\u00a096, 4285\u20134288 (1999)","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"6_CR13","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1093\/nar\/30.1.38","volume":"30","author":"T. Hubbard","year":"2002","unstructured":"Hubbard, T., Barker, D., Birney, E., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T., Durbin, R., Eyras, E., Gilbert, J., Hammond, M., Huminiecki, L., Kasprzyk, A., Lehvaslaiho, H., Lijnzaad, P., Melsopp, C., Mongin, E., Pettett, R., Pocock, M., Potter, S., Rust, A., Schmidt, E., Searle, S., Slater, G., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Stupka, E., Ureta-Vidal, A., Vastrik, I., Clamp, M.: The Ensembl genome database project. Nucleic Acids Res.\u00a030, 38\u201341 (2002)","journal-title":"Nucleic Acids Res."},{"key":"6_CR14","first-page":"34","volume":"33 Database Iss","author":"D.A. Benson","year":"2005","unstructured":"Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L.: GenBank. Nucleic Acids Res.\u00a033 Database Issue, 34\u201338 (2005)","journal-title":"Nucleic Acids Res"},{"key":"6_CR15","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/bioinformatics\/16.2.101","volume":"16","author":"G.H. Gonnet","year":"2000","unstructured":"Gonnet, G.H., Hallett, M.T., Korostensky, C., Bernardin, L.: Darwin v. 2.0 an interpreted computer language for the biosciences. Bioinformatics\u00a016, 101\u2013103 (2000)","journal-title":"Bioinformatics"},{"key":"6_CR16","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/S1476-9271(02)00094-4","volume":"27","author":"A. Gattiker","year":"2003","unstructured":"Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A.H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C.J.A., Lachaize, C., Veuthey, A.L., Gasteiger, E., Bairoch, A.: Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem.\u00a027, 49\u201358 (2003)","journal-title":"Comput. Biol. Chem."},{"key":"6_CR17","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/nar\/gkg095","volume":"31","author":"B. Boeckmann","year":"2003","unstructured":"Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O\u2019Donovan, C., Phan, I., Pilbout, S., Schneider, M.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res.\u00a031, 365\u2013370 (2003)","journal-title":"Nucleic Acids Res."},{"key":"6_CR18","doi-asserted-by":"publisher","first-page":"1443","DOI":"10.1126\/science.1604319","volume":"256","author":"G.H. Gonnet","year":"1992","unstructured":"Gonnet, G.H., Cohen, M.A., Benner, S.A.: Exhaustive matching of the entire protein sequence database. Science\u00a0256, 1443\u20131445 (1992)","journal-title":"Science"},{"key":"6_CR19","unstructured":"Gonnet, G.H.: A tutorial introduction to computational biochemistry using Darwin. Technical report, Informatik, ETH Zurich, Switzerland (1994)"},{"key":"6_CR20","doi-asserted-by":"publisher","first-page":"6073","DOI":"10.1073\/pnas.95.11.6073","volume":"95","author":"S.E. Brenner","year":"1998","unstructured":"Brenner, S.E., Chothia, C., Hubbard, J.T.: Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. U. S. A.\u00a095, 6073\u20136078 (1998)","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"6_CR21","first-page":"433","volume":"33 Database Iss","author":"C. Mering von","year":"2005","unstructured":"von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A., Bork, P.: STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res.\u00a033 Database Issue, 433\u2013437 (2005)","journal-title":"Nucleic Acids Res"},{"key":"6_CR22","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/S0020-0190(97)00213-5","volume":"65","author":"R. Balasubramanian","year":"1998","unstructured":"Balasubramanian, R., Fellows, M.R., Raman, V.: An improved fixed-parameter algorithm for vertex cover. Inf. Process. Lett.\u00a065, 163\u2013168 (1998)","journal-title":"Inf. Process. Lett."},{"key":"6_CR23","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1093\/nar\/28.1.304","volume":"28","author":"A. Bairoch","year":"2000","unstructured":"Bairoch, A.: The ENZYME database in 2000. Nucleic Acids Res.\u00a028, 304\u2013305 (2000)","journal-title":"Nucleic Acids Res"},{"key":"6_CR24","unstructured":"Jensen, R.A.: Orthologs and paralogs - we need to get it right. Genome. Biol. 2, INTERACTIONS1002 (2001)"},{"key":"6_CR25","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1016\/j.sbi.2004.03.011","volume":"14","author":"C. Vogel","year":"2004","unstructured":"Vogel, C., Bashton, M., Kerrison, N.D., Chothia, C., Teichmann, S.A.: Structure, function and evolution of multidomain proteins. Curr. Opin. Struct. Biol.\u00a014, 208\u2013216 (2004)","journal-title":"Curr Opin Struct Biol"}],"container-title":["Lecture Notes in Computer Science","Comparative Genomics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/11554714_6.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T07:06:57Z","timestamp":1619507217000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/11554714_6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005]]},"ISBN":["9783540289326","9783540318149"],"references-count":25,"URL":"https:\/\/doi.org\/10.1007\/11554714_6","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2005]]}}}