{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T10:12:52Z","timestamp":1761559972108},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Although many genomic features have been used in the prediction of protein-protein interactions (PPIs), frequently only one is used in a computational method. After realizing the limited power in the prediction using only one genomic feature, investigators are now moving toward integration. So far, there have been few integration studies for PPI prediction; one failed to yield appreciable improvement of prediction and the others did not conduct performance comparison. It remains unclear whether an integration of multiple genomic features can improve the PPI prediction and, if it can, how to integrate these features.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this study, we first performed a systematic evaluation on the PPI prediction in <jats:italic>Escherichia coli<\/jats:italic> (<jats:italic>E. coli<\/jats:italic>) by four genomic context based methods: the phylogenetic profile method, the gene cluster method, the gene fusion method, and the gene neighbor method. The number of predicted PPIs and the average degree in the predicted PPI networks varied greatly among the four methods. Further, no method outperformed the others when we tested using three well-defined positive datasets from the KEGG, EcoCyc, and DIP databases. Based on these comparisons, we developed a novel integrated method, named InPrePPI. InPrePPI first normalizes the <jats:italic>AC<\/jats:italic> value (an integrated value of the accuracy and coverage) of each method using three positive datasets, then calculates a weight for each method, and finally uses the weight to calculate an integrated score for each protein pair predicted by the four genomic context based methods. We demonstrate that InPrePPI outperforms each of the four individual methods and, in general, the other two existing integrated methods: the joint observation method and the integrated prediction method in STRING. These four methods and InPrePPI are implemented in a user-friendly web interface.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>This study evaluated the PPI prediction by four genomic context based methods, and presents an integrated evaluation method that shows better performance in <jats:italic>E. coli<\/jats:italic>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-414","type":"journal-article","created":{"date-parts":[[2007,10,26]],"date-time":"2007-10-26T16:40:06Z","timestamp":1193416806000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes"],"prefix":"10.1186","volume":"8","author":[{"given":"Jingchun","family":"Sun","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guohui","family":"Ding","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Youyu","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tieliu","family":"Shi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yixue","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongming","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,10,26]]},"reference":[{"key":"1786_CR1","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1002\/1615-9861(200206)2:6<611::AID-PROT611>3.0.CO;2-Y","volume":"2","author":"D Auerbach","year":"2002","unstructured":"Auerbach D, Thaminy S, Hottiger MO, Stagljar I: The post-genomic era of interactive proteomics: facts and perspectives. Proteomics 2002, 2: 611\u2013623. 10.1002\/1615-9861(200206)2:6<611::AID-PROT611>3.0.CO;2-Y","journal-title":"Proteomics"},{"key":"1786_CR2","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/35015694","volume":"405","author":"D Eisenberg","year":"2000","unstructured":"Eisenberg D, Marcotte EM, Xenarios I, Yeates TO: Protein function in the post-genomic era. Nature 2000, 405: 823\u2013826. 10.1038\/35015694","journal-title":"Nature"},{"key":"1786_CR3","doi-asserted-by":"publisher","first-page":"R59","DOI":"10.1186\/gb-2003-4-9-r59","volume":"4","author":"M Strong","year":"2003","unstructured":"Strong M, Mallick P, Pellegrini M, Thompson M, Eisenberg D: Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol 2003, 4: R59. 10.1186\/gb-2003-4-9-r59","journal-title":"Genome Biol"},{"key":"1786_CR4","doi-asserted-by":"publisher","first-page":"R63","DOI":"10.1186\/gb-2004-5-9-r63","volume":"5","author":"B Lehner","year":"2004","unstructured":"Lehner B, Fraser AG: A first-draft human protein-interaction map. Genome Biol 2004, 5: R63. 10.1186\/gb-2004-5-9-r63","journal-title":"Genome Biol"},{"key":"1786_CR5","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/35051615","volume":"409","author":"JC Rain","year":"2001","unstructured":"Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schachter V, Chemama Y, Labigne A, Legrain P: The protein-protein interaction map of Helicobacter pylori. Nature 2001, 409: 211\u2013215. 10.1038\/35051615","journal-title":"Nature"},{"key":"1786_CR6","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.1038\/82360","volume":"18","author":"B Schwikowski","year":"2000","unstructured":"Schwikowski B, Uetz P, Fields S: A network of protein-protein interactions in yeast. Nat Biotechnol 2000, 18: 1257\u20131261. 10.1038\/82360","journal-title":"Nat Biotechnol"},{"key":"1786_CR7","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1126\/science.1091403","volume":"303","author":"S Li","year":"2004","unstructured":"Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M: A map of the interactome network of the metazoan C. elegans. Science 2004, 303: 540\u2013543. 10.1126\/science.1091403","journal-title":"Science"},{"key":"1786_CR8","doi-asserted-by":"publisher","first-page":"1727","DOI":"10.1126\/science.1090289","volume":"302","author":"L Giot","year":"2003","unstructured":"Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL Jr., White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM: A protein interaction map of Drosophila melanogaster. Science 2003, 302: 1727\u20131736. 10.1126\/science.1090289","journal-title":"Science"},{"key":"1786_CR9","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","volume":"122","author":"U Stelzl","year":"2005","unstructured":"Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksoz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE: A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122: 957\u2013968. 10.1016\/j.cell.2005.08.029","journal-title":"Cell"},{"key":"1786_CR10","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1038\/47048","volume":"402","author":"EM Marcotte","year":"1999","unstructured":"Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D: A combined algorithm for genome-wide prediction of protein function. Nature 1999, 402: 83\u201386. 10.1038\/47048","journal-title":"Nature"},{"key":"1786_CR11","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/35048107","volume":"2","author":"AJ Walhout","year":"2001","unstructured":"Walhout AJ, Vidal M: Protein interaction maps for model organisms. Nat Rev Mol Cell Biol 2001, 2: 55\u201362. 10.1038\/35048107","journal-title":"Nat Rev Mol Cell Biol"},{"key":"1786_CR12","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/nature750","volume":"417","author":"C von Mering","year":"2002","unstructured":"von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417: 399\u2013403. 10.1038\/nature750","journal-title":"Nature"},{"key":"1786_CR13","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1002\/prot.20865","volume":"63","author":"Y Qi","year":"2006","unstructured":"Qi Y, Bar-Joseph Z, Klein-Seetharaman J: Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 2006, 63: 490\u2013500. 10.1002\/prot.20865","journal-title":"Proteins"},{"key":"1786_CR14","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 EM, Thompson MJ, Eisenberg D, Yeates TO: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96: 4285\u20134288. 10.1073\/pnas.96.8.4285","journal-title":"Proc Natl Acad Sci USA"},{"key":"1786_CR15","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1038\/47056","volume":"402","author":"AJ Enright","year":"1999","unstructured":"Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA: Protein interaction maps for complete genomes based on gene fusion events. Nature 1999, 402: 86\u201390. 10.1038\/47056","journal-title":"Nature"},{"key":"1786_CR16","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1016\/S0968-0004(98)01274-2","volume":"23","author":"T Dandekar","year":"1998","unstructured":"Dandekar T, Snel B, Huynen M, Bork P: Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 1998, 23: 324\u2013328. 10.1016\/S0968-0004(98)01274-2","journal-title":"Trends Biochem Sci"},{"key":"1786_CR17","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1101\/gr.10.8.1204","volume":"10","author":"M Huynen","year":"2000","unstructured":"Huynen M, Snel B, Lathe W 3rd, Bork P: Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 2000, 10: 1204\u20131210. 10.1101\/gr.10.8.1204","journal-title":"Genome Res"},{"key":"1786_CR18","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/S0955-0674(03)00009-7","volume":"15","author":"MA Huynen","year":"2003","unstructured":"Huynen MA, Snel B, von Mering C, Bork P: Function prediction and protein networks. Curr Opin Cell Biol 2003, 15: 191\u2013198. 10.1016\/S0955-0674(03)00009-7","journal-title":"Curr Opin Cell Biol"},{"key":"1786_CR19","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1126\/science.1068664","volume":"295","author":"M Gerstein","year":"2002","unstructured":"Gerstein M, Lan N, Jansen R: Enhanced: integrating interactomes. Science 2002, 295: 284\u2013287. 10.1126\/science.1068664","journal-title":"Science"},{"key":"1786_CR20","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1109\/51.940042","volume":"20","author":"P Bertone","year":"2001","unstructured":"Bertone P, Gerstein M: Integrative data mining: the new direction in bioinformatics. IEEE Eng Med Biol Mag 2001, 20: 33\u201340. 10.1109\/51.940042","journal-title":"IEEE Eng Med Biol Mag"},{"key":"1786_CR21","doi-asserted-by":"publisher","first-page":"159","DOI":"10.2174\/1389203033487225","volume":"4","author":"Y Chen","year":"2003","unstructured":"Chen Y, Xu D: Computational analyses of high-throughput protein-protein interaction data. Curr Protein Pept Sci 2003, 4: 159\u2013181. 10.2174\/1389203033487225","journal-title":"Curr Protein Pept Sci"},{"key":"1786_CR22","doi-asserted-by":"publisher","first-page":"D433","DOI":"10.1093\/nar\/gki005","volume":"33","author":"C von Mering","year":"2005","unstructured":"von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P: STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res 2005, 33: D433\u20137. 10.1093\/nar\/gki005","journal-title":"Nucleic Acids Res"},{"key":"1786_CR23","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/35001009","volume":"403","author":"P Uetz","year":"2000","unstructured":"Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403: 623\u2013627. 10.1038\/35001009","journal-title":"Nature"},{"key":"1786_CR24","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/S0959-440X(03)00070-8","volume":"13","author":"L Salwinski","year":"2003","unstructured":"Salwinski L, Eisenberg D: Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol 2003, 13: 377\u2013382. 10.1016\/S0959-440X(03)00070-8","journal-title":"Curr Opin Struct Biol"},{"key":"1786_CR25","unstructured":"KEGG Database[http:\/\/www.genome.jp\/kegg\/]"},{"key":"1786_CR26","unstructured":"EcoCyc Database[http:\/\/ecocyc.org\/]"},{"key":"1786_CR27","unstructured":"DIP Database[http:\/\/dip.doe-mbi.ucla.edu\/]"},{"key":"1786_CR28","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nrg1272","volume":"5","author":"AL Barabasi","year":"2004","unstructured":"Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5: 101\u2013113. 10.1038\/nrg1272","journal-title":"Nat Rev Genet"},{"key":"1786_CR29","doi-asserted-by":"publisher","first-page":"4157","DOI":"10.1093\/nar\/gkg466","volume":"31","author":"A Grigoriev","year":"2003","unstructured":"Grigoriev A: On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res 2003, 31: 4157\u20134161. 10.1093\/nar\/gkg466","journal-title":"Nucleic Acids Res"},{"key":"1786_CR30","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1126\/science.285.5428.751","volume":"285","author":"EM Marcotte","year":"1999","unstructured":"Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D: Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285: 751\u2013753. 10.1126\/science.285.5428.751","journal-title":"Science"},{"key":"1786_CR31","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/79847","volume":"26","author":"S Tsoka","year":"2000","unstructured":"Tsoka S, Ouzounis CA: Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nat Genet 2000, 26: 141\u2013142. 10.1038\/79847","journal-title":"Nat Genet"},{"key":"1786_CR32","unstructured":"InPrePPI[http:\/\/www.biosino.org\/InPrePPI\/]"},{"key":"1786_CR33","doi-asserted-by":"publisher","first-page":"R35","DOI":"10.1186\/gb-2004-5-5-r35","volume":"5","author":"PM Bowers","year":"2004","unstructured":"Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D: Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 2004, 5: R35. 10.1186\/gb-2004-5-5-r35","journal-title":"Genome Biol"},{"key":"1786_CR34","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/gb-2002-3-11-research0060","volume":"3","author":"Y Zheng","year":"2002","unstructured":"Zheng Y, Roberts RJ, Kasif S: Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol 2002, 3: R60. 10.1186\/gb-2002-3-11-research0060","journal-title":"Genome Biol"},{"key":"1786_CR35","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1101\/gr.3610305","volume":"15","author":"LJ Lu","year":"2005","unstructured":"Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M: Assessing the limits of genomic data integration for predicting protein networks. Genome Res 2005, 15: 945\u2013953. 10.1101\/gr.3610305","journal-title":"Genome Res"},{"key":"1786_CR36","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1016\/j.bbrc.2006.12.146","volume":"353","author":"J Sun","year":"2007","unstructured":"Sun J, Li Y, Zhao Z: Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochem Biophys Res Commun 2007, 353: 985\u2013991. 10.1016\/j.bbrc.2006.12.146","journal-title":"Biochem Biophys Res Commun"},{"key":"1786_CR37","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1186\/1471-2105-8-173","volume":"8","author":"R Jothi","year":"2007","unstructured":"Jothi R, Przytycka TM, Aravind L: Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 2007, 8: 173. 10.1186\/1471-2105-8-173","journal-title":"BMC Bioinformatics"},{"key":"1786_CR38","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1016\/j.bbrc.2007.02.048","volume":"355","author":"J Sun","year":"2007","unstructured":"Sun J, Zhao Z: Construction of phylogenetic profiles based on the genetic distance of hundreds of genomes. Biochem Biophys Res Commun 2007, 355: 849\u2013853. 10.1016\/j.bbrc.2007.02.048","journal-title":"Biochem Biophys Res Commun"},{"key":"1786_CR39","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1101\/gr.553803","volume":"13","author":"MJ Lercher","year":"2003","unstructured":"Lercher MJ, Blumenthal T, Hurst LD: Coexpression of neighboring genes in Caenorhabditis Elegans is mostly due to operons and duplicate genes. Genome Res 2003, 13: 238\u2013243. 10.1101\/gr.553803","journal-title":"Genome Res"},{"key":"1786_CR40","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1101\/gr.2131104","volume":"14","author":"EJ Williams","year":"2004","unstructured":"Williams EJ, Bowles DJ: Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Res 2004, 14: 1060\u20131067. 10.1101\/gr.2131104","journal-title":"Genome Res"},{"key":"1786_CR41","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/ng887","volume":"31","author":"MJ Lercher","year":"2002","unstructured":"Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002, 31: 180\u2013183. 10.1038\/ng887","journal-title":"Nat Genet"},{"key":"1786_CR42","doi-asserted-by":"publisher","first-page":"e42","DOI":"10.1371\/journal.pcbi.0030042","volume":"3","author":"BA Shoemaker","year":"2007","unstructured":"Shoemaker BA, Panchenko AR: Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol 2007, 3: e42. 10.1371\/journal.pcbi.0030042","journal-title":"PLoS Comput Biol"},{"key":"1786_CR43","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1101\/gr.205602","volume":"12","author":"R Jansen","year":"2002","unstructured":"Jansen R, Greenbaum D, Gerstein M: Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12: 37\u201346. 10.1101\/gr.205602","journal-title":"Genome Res"},{"key":"1786_CR44","unstructured":"NCBI RefSeq Database[ftp:\/\/ftp.ncbi.nih.gov\/genomes\/]"},{"key":"1786_CR45","unstructured":"SHOPS[http:\/\/bioinformatics.holstegelab.nl\/services\/shops\/]"},{"key":"1786_CR46","unstructured":"STRING[http:\/\/string.embl.de\/]"},{"key":"1786_CR47","unstructured":"NCBI E. coli COG Annotations[ftp:\/\/ftp.ncbi.nih.gov\/genomes\/Bacteria\/Escherichia_coli_K12\/]"},{"key":"1786_CR48","doi-asserted-by":"publisher","first-page":"3409","DOI":"10.1093\/bioinformatics\/bti532","volume":"21","author":"J Sun","year":"2005","unstructured":"Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y: Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics 2005, 21: 3409\u20133415. 10.1093\/bioinformatics\/bti532","journal-title":"Bioinformatics"},{"key":"1786_CR49","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997, 25: 3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucl Acids Res"},{"key":"1786_CR50","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1038\/nbt861","volume":"21","author":"SV Date","year":"2003","unstructured":"Date SV, Marcotte EM: Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol 2003, 21: 1055\u20131062. 10.1038\/nbt861","journal-title":"Nat Biotechnol"},{"key":"1786_CR51","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1073\/pnas.96.6.2896","volume":"96","author":"R Overbeek","year":"1999","unstructured":"Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N: The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 1999, 96: 2896\u20132901. 10.1073\/pnas.96.6.2896","journal-title":"Proc Natl Acad Sci USA"},{"key":"1786_CR52","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22: 4673\u20134680. 10.1093\/nar\/22.22.4673","journal-title":"Nucleic Acids Res"},{"key":"1786_CR53","first-page":"164","volume":"5","author":"J Felsenstein","year":"1989","unstructured":"Felsenstein J: PHYLIP - phylogeny inference package (version 3.2). Cladistics 1989, 5: 164\u2013166.","journal-title":"Cladistics"},{"key":"1786_CR54","unstructured":"KEGG Orthology (KO)[http:\/\/www.genome.jp\/dbget-bin\/get_htext?KO+-s+F+-f+F\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-414.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T01:44:54Z","timestamp":1630460694000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-414"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,10,26]]},"references-count":54,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1786"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-414","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,10,26]]},"assertion":[{"value":"30 March 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 October 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 October 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"414"}}