{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T14:38:34Z","timestamp":1780411114658,"version":"3.54.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics.<\/jats:p><jats:p>Results: We have created a Genome Properties system to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties.<\/jats:p><jats:p>Availability: Genome Properties can be found at http:\/\/www.tigr.org\/Genome_Properties<\/jats:p><jats:p>Contact: \u00a0selengut@tigr.org<\/jats:p><jats:p>Supplementary information: \u00a0http:\/\/www.tigr.org\/tigr-scripts\/CMR2\/genome_properties_references.spl<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti015","type":"journal-article","created":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T07:33:02Z","timestamp":1094542382000},"page":"293-306","source":"Crossref","is-referenced-by-count":62,"title":["Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics"],"prefix":"10.1093","volume":"21","author":[{"given":"Daniel H.","family":"Haft","sequence":"first","affiliation":[{"name":"The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy D.","family":"Selengut","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren M.","family":"Brinkac","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikhat","family":"Zafar","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Owen","family":"White","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2004,9,3]]},"reference":[{"key":"2023051305563483400_B1","unstructured":"Andersson, J.O. and Andersson, S.G. 1999Genome degradation is an ongoing process in Rickettsia. Mol. Biol. Evol.161178\u20131191"},{"key":"2023051305563483400_B2","unstructured":"Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L. 2004The Pfam protein families database. Nucleic Acids Res.32D138\u2013D141"},{"key":"2023051305563483400_B3","doi-asserted-by":"crossref","unstructured":"Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., Pilbout, S., Schneider, M. 2003The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res.31365\u2013370","DOI":"10.1093\/nar\/gkg095"},{"key":"2023051305563483400_B4","doi-asserted-by":"crossref","unstructured":"Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., Ehrlich, S.D., Sorokin, A. 2001The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res.11731\u2013753","DOI":"10.1101\/gr.GR-1697R"},{"key":"2023051305563483400_B5","doi-asserted-by":"crossref","unstructured":"Clark, M.A., Baumann, L., Baumann, P. 1998Buchnera aphidicola (Aphid endosymbiont) contains genes encoding enzymes of histidine biosynthesis. Curr. Microbiol.37356\u2013358","DOI":"10.1007\/s002849900392"},{"key":"2023051305563483400_B6","unstructured":"Delcher, A.L., Harmon, D., Kasif, S., White, O., Salzberg, S.L. 1999Improved microbial gene identification with GLIMMER. Nucleic Acids Res.274636\u20134641"},{"key":"2023051305563483400_B7","doi-asserted-by":"crossref","unstructured":"Farabaugh, P.J. 2000Translational frameshifting: implications for the mechanism of translational frame maintenance. Prog. Nucleic Acid Res. Mol. Biol.64131\u2013170","DOI":"10.1016\/S0079-6603(00)64004-7"},{"key":"2023051305563483400_B8","doi-asserted-by":"crossref","unstructured":"Finkel, S.E. and Kolter, R. 2001DNA as a nutrient: novel role for bacterial competence gene homologs. J. Bacteriol.1836288\u20136293","DOI":"10.1128\/JB.183.21.6288-6293.2001"},{"key":"2023051305563483400_B9","unstructured":"Fitch, W.M. 1970Distinguishing homologous from analogous proteins. Syst. Zool.1999\u2013113"},{"key":"2023051305563483400_B10","unstructured":"Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., et al. 1995Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science269496\u2013512"},{"key":"2023051305563483400_B11","unstructured":"Fleischmann, R.D., Alland, D., Eisen, J.A., Carpenter, L., White, O., Peterson, J., DeBoy, R., Dodson, R., Gwinn, M., Haft, D., et al. 2002Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol.1845479\u20135490"},{"key":"2023051305563483400_B12","doi-asserted-by":"crossref","unstructured":"Graupner, M. and White, R.H. 2001Methanococcus jannaschii generates l-proline by cyclization of l-ornithine. J. Bacteriol.1835203\u20135205","DOI":"10.1128\/JB.183.17.5203-5205.2001"},{"key":"2023051305563483400_B13","unstructured":"Haft, D.H., Loftus, B.J., Richardson, D.L., Yang, F., Eisen, J.A., Paulsen, I.T., White, O. 2001TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res.2941\u201343"},{"key":"2023051305563483400_B14","doi-asserted-by":"crossref","unstructured":"Haft, D.H., Selengut, J.D., White, O. 2003The TIGRFAMs database of protein families. Nucleic Acids Res.31371\u2013373","DOI":"10.1093\/nar\/gkg128"},{"key":"2023051305563483400_B15","doi-asserted-by":"crossref","unstructured":"Harris, M.A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C. 2004The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res.32D258\u2013D261","DOI":"10.1093\/nar\/gkh036"},{"key":"2023051305563483400_B16","unstructured":"Hulo, N., Sigrist, C.J., Le Saux, V., Langendijk-Genevaux, P.S., Bordoli, L., Gattiker, A., De Castro, E., Bucher, P., Bairoch, A. 2004Recent improvements to the PROSITE database. Nucleic Acids Res.32D134\u2013D137"},{"key":"2023051305563483400_B17","doi-asserted-by":"crossref","unstructured":"Kalinowski, J., Bathe, B., Bartels, D., Bischoff, N., Bott, M., Burkovski, A., Dusch, N., Eggeling, L., Eikmanns, B.J., Gaigalat, L. 2003The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins. J. Biotechnol.1045\u201325","DOI":"10.1016\/S0168-1656(03)00154-8"},{"key":"2023051305563483400_B18","doi-asserted-by":"crossref","unstructured":"Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M. 2004The KEGG resource for deciphering the genome. Nucleic Acids Res.32D277\u2013D280","DOI":"10.1093\/nar\/gkh063"},{"key":"2023051305563483400_B19","doi-asserted-by":"crossref","unstructured":"Karp, P.D., Paley, S., Romero, P. 2002The Pathway Tools software. Bioinformatics18(Suppl. 1),S225\u2013S232","DOI":"10.1093\/bioinformatics\/18.suppl_1.S225"},{"key":"2023051305563483400_B20","unstructured":"Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A. 2002The MetaCyc Database. Nucleic Acids Res.3059\u201361"},{"key":"2023051305563483400_B21","unstructured":"Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S.M., Pellegrini-Toole, A., Bonavides, C., Gama-Castro, S. 2002The EcoCyc Database. Nucleic Acids Res.3056\u201358"},{"key":"2023051305563483400_B22","unstructured":"Koonin, E.V., Mushegian, A.R., Bork, P. 1996Non-orthologous gene displacement. Trends Genet.12334\u2013336"},{"key":"2023051305563483400_B23","doi-asserted-by":"crossref","unstructured":"Lowe, T.M. and Eddy, S.R. 1997tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res.25955\u2013964","DOI":"10.1093\/nar\/25.5.955"},{"key":"2023051305563483400_B24","unstructured":"(Ed.). Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology1999, NY John Wiley and Sons"},{"key":"2023051305563483400_B25","doi-asserted-by":"crossref","unstructured":"McGarvey, P.B., Huang, H., Barker, W.C., Orcutt, B.C., Garavelli, J.S., Srinivasarao, G.Y., Yeh, L.S., Xiao, C., Wu, C.H. 2000PIR: a new resource for bioinformatics. Bioinformatics16, pp. 290\u2013291","DOI":"10.1093\/bioinformatics\/16.3.290"},{"key":"2023051305563483400_B26","unstructured":"Osterman, A. and Overbeek, R. 2003Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol.7238\u2013251"},{"key":"2023051305563483400_B27","doi-asserted-by":"crossref","unstructured":"Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D., Maltsev, N. 1999The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA962896\u20132901","DOI":"10.1073\/pnas.96.6.2896"},{"key":"2023051305563483400_B28","unstructured":"Overbeek, R., Larsen, N., Pusch, G.D., D'Souza, M., Selkov, E., Jr, Kyrpides, N., Fonstein, M., Maltsev, N., Selkov, E. 2000WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res.28123\u2013125"},{"key":"2023051305563483400_B29","unstructured":"Overbeek, R., Larsen, N., Walunas, T., D'Souza, M., Pusch, G., Selkov, E., Jr, Liolios, K., Joukov, V., Kaznadzey, D., Anderson, I. 2003The ERGO genome analysis and discovery system. Nucleic Acids Res.31164\u2013171"},{"key":"2023051305563483400_B30","doi-asserted-by":"crossref","unstructured":"Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D., Yeates, T.O. 1999Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci., USA964285\u20134288","DOI":"10.1073\/pnas.96.8.4285"},{"key":"2023051305563483400_B31","unstructured":"Peterson, J.D., Umayam, L.A., Dickinson, T., Hickey, E.K., White, O. 2001The Comprehensive Microbial Resource. Nucleic Acids Res.29123\u2013125"},{"key":"2023051305563483400_B32","doi-asserted-by":"crossref","unstructured":"Ren, Q., Kang, K.H., Paulsen, I.T. 2004TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res.32D284\u2013D288","DOI":"10.1093\/nar\/gkh016"},{"key":"2023051305563483400_B33","doi-asserted-by":"crossref","unstructured":"Roten, C.A., Gamba, P., Barblan, J.L., Karamata, D. 2002Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes. Nucleic Acids Res.30142\u2013144","DOI":"10.1093\/nar\/30.1.142"},{"key":"2023051305563483400_B34","unstructured":"Stadtman, T.C. 1987Specific occurrence of selenium in enzymes and amino acid tRNAs. FASEB J.1375\u2013379"},{"key":"2023051305563483400_B35","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. 2003The COG database: an updated version includes eukaryotes. BMC Bioinformatics441","DOI":"10.1186\/1471-2105-4-41"},{"key":"2023051305563483400_B36","unstructured":"Tekaia, F., Yeramian, E., Dujon, B. 2002Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene29751\u201360"},{"key":"2023051305563483400_B37","unstructured":"van Nimwegen, E. 2003Scaling laws in the functional content of genomes. Trends Genet.19479\u2013484"},{"key":"2023051305563483400_B38","unstructured":"Wheeler, D.L., Church, D.M., Edgar, R., Federhen, S., Helmberg, W., Madden, T.L., Pontius, J.U., Schuler, G.D., Schriml, L.M., Sequeira, E. 2004Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res.32D35\u2013D40"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/3\/293\/50305660\/bioinformatics_21_3_293.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/3\/293\/50305660\/bioinformatics_21_3_293.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T14:24:10Z","timestamp":1734531850000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/3\/293\/238015"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,9,3]]},"references-count":38,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2005,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti015","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,2,1]]},"published":{"date-parts":[[2004,9,3]]}}}