{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T15:26:21Z","timestamp":1784733981890,"version":"3.55.0"},"reference-count":40,"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":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest. Recently, multiple programs for automated detection of GIs have been developed that utilize sequence composition characteristics, such as G+C ratio and dinucleotide bias. To robustly evaluate the accuracy of such methods, we propose that a dataset of GIs be constructed using criteria that are independent of sequence composition-based analysis approaches.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed a comparative genomics approach (IslandPick) that identifies both very probable islands and non-island regions. The approach involves 1) flexible, automated selection of comparative genomes for each query genome, using a distance function that picks appropriate genomes for identification of GIs, 2) identification of regions unique to the query genome, compared with the chosen genomes (positive dataset) and 3) identification of regions conserved across all genomes (negative dataset). Using our constructed datasets, we investigated the accuracy of several sequence composition-based GI prediction tools.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Our results indicate that AlienHunter has the highest recall, but the lowest measured precision, while SIGI-HMM is the most precise method. SIGI-HMM and IslandPath\/DIMOB have comparable overall highest accuracy. Our comparative genomics approach, IslandPick, was the most accurate, compared with a curated list of GIs, indicating that we have constructed suitable datasets. This represents the first evaluation, using diverse and, independent datasets that were not artificially constructed, of the accuracy of several sequence composition-based GI predictors. The caveats associated with this analysis and proposals for optimal island prediction are discussed.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-329","type":"journal-article","created":{"date-parts":[[2008,8,5]],"date-time":"2008-08-05T06:15:46Z","timestamp":1217916946000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":247,"title":["Evaluation of genomic island predictors using a comparative genomics approach"],"prefix":"10.1186","volume":"9","author":[{"given":"Morgan GI","family":"Langille","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William WL","family":"Hsiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fiona SL","family":"Brinkman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2008,8,5]]},"reference":[{"key":"2314_CR1","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1038\/nature04160","volume":"437","author":"CA Suttle","year":"2005","unstructured":"Suttle CA: Viruses in the sea. Nature 2005, 437: 356\u2013361. 10.1038\/nature04160","journal-title":"Nature"},{"key":"2314_CR2","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/35012500","volume":"405","author":"H Ochman","year":"2000","unstructured":"Ochman H, Lawrence JG, Groisman EA: Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405: 299\u2013304. 10.1038\/35012500","journal-title":"Nature"},{"key":"2314_CR3","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1146\/annurev.micro.54.1.641","volume":"54","author":"J Hacker","year":"2000","unstructured":"Hacker J, Kaper JB: Pathogenicity islands and the evolution of microbes. Annual Review of Microbiology 2000, 54: 641\u2013679. 10.1146\/annurev.micro.54.1.641","journal-title":"Annual Review of Microbiology"},{"key":"2314_CR4","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1038\/nrmicro884","volume":"2","author":"U Dobrindt","year":"2004","unstructured":"Dobrindt U, Hochhut B, Hentschel U, Hacker J: Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2004, 2: 414\u2013424. 10.1038\/nrmicro884","journal-title":"Nat Rev Microbiol"},{"key":"2314_CR5","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1128\/CMR.17.1.14-56.2004","volume":"17","author":"H Schmidt","year":"2004","unstructured":"Schmidt H, Hensel M: Pathogenicity islands in bacterial pathogenesis. Clin Microbiol Rev 2004, 17: 14\u201356. 10.1128\/CMR.17.1.14-56.2004","journal-title":"Clin Microbiol Rev"},{"key":"2314_CR6","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/0882-4010(90)90048-U","volume":"8","author":"J Hacker","year":"1990","unstructured":"Hacker J, Bender L, Ott M, Wingender J, Lund B, Marre R, Goebel W: Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates. Microb Pathog 1990, 8: 213\u2013225. 10.1016\/0882-4010(90)90048-U","journal-title":"Microb Pathog"},{"key":"2314_CR7","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1016\/S0966-842X(01)02079-0","volume":"9","author":"S Karlin","year":"2001","unstructured":"Karlin S: Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends In microbiology 2001, 9: 335\u2013343. 10.1016\/S0966-842X(01)02079-0","journal-title":"Trends In microbiology"},{"key":"2314_CR8","doi-asserted-by":"publisher","first-page":"e62","DOI":"10.1371\/journal.pgen.0010062","volume":"1","author":"WW Hsiao","year":"2005","unstructured":"Hsiao WW, Ung K, Aeschliman D, Bryan J, Finlay BB, Brinkman FS: Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet 2005, 1: e62. 10.1371\/journal.pgen.0010062","journal-title":"PLoS Genet"},{"key":"2314_CR9","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1101\/gr.7004508","volume":"18","author":"GS Vernikos","year":"2008","unstructured":"Vernikos GS, Parkhill J: Resolving the structural features of genomic islands: a machine learning approach. Genome Res 2008, 18: 331\u2013342. 10.1101\/gr.7004508","journal-title":"Genome Res"},{"key":"2314_CR10","doi-asserted-by":"publisher","first-page":"1089","DOI":"10.1046\/j.1365-2958.1997.3101672.x","volume":"23","author":"J Hacker","year":"1997","unstructured":"Hacker J, Blum-Oehler G, Muhldorfer I, Tschape H: Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Molecular Microbiology 1997, 23: 1089\u20131097. 10.1046\/j.1365-2958.1997.3101672.x","journal-title":"Molecular Microbiology"},{"key":"2314_CR11","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1093\/bioinformatics\/btg004","volume":"19","author":"W Hsiao","year":"2003","unstructured":"Hsiao W, Wan I, Jones SJ, Brinkman FS: IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003, 19: 418\u2013420. 10.1093\/bioinformatics\/btg004","journal-title":"Bioinformatics"},{"key":"2314_CR12","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/S0378-1097(03)00204-0","volume":"221","author":"Q Tu","year":"2003","unstructured":"Tu Q, Ding D: Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis. FEMS Microbiology Letters 2003, 221: 269\u2013275. 10.1016\/S0378-1097(03)00204-0","journal-title":"FEMS Microbiology Letters"},{"key":"2314_CR13","doi-asserted-by":"publisher","first-page":"D55","DOI":"10.1093\/nar\/gkh059","volume":"32","author":"Y Mantri","year":"2004","unstructured":"Mantri Y, Williams KP: Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Research 2004, 32: D55\u20138. 10.1093\/nar\/gkh059","journal-title":"Nucleic Acids Research"},{"key":"2314_CR14","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/1471-2105-5-22","volume":"5","author":"R Merkl","year":"2004","unstructured":"Merkl R: SIGI: score-based identification of genomic islands. BMC Bioinformatics 2004, 5: 22. 10.1186\/1471-2105-5-22","journal-title":"BMC Bioinformatics"},{"key":"2314_CR15","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1093\/bioinformatics\/btl369","volume":"22","author":"GS Vernikos","year":"2006","unstructured":"Vernikos GS, Parkhill J: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 2006, 22: 2196\u20132203. 10.1093\/bioinformatics\/btl369","journal-title":"Bioinformatics"},{"key":"2314_CR16","doi-asserted-by":"publisher","first-page":"2672","DOI":"10.1093\/bioinformatics\/btm405","volume":"23","author":"I Rajan","year":"2007","unstructured":"Rajan I, Aravamuthan S, Mande SS: Identification of compositionally distinct regions in genomes using the centroid method. Bioinformatics 2007, 23: 2672\u20132677. 10.1093\/bioinformatics\/btm405","journal-title":"Bioinformatics"},{"key":"2314_CR17","doi-asserted-by":"publisher","first-page":"1341","DOI":"10.1046\/j.1365-2958.1998.01008.x","volume":"29","author":"S Karlin","year":"1998","unstructured":"Karlin S, Mrazek J, Campbell AM: Codon usages in different gene classes of the Escherichia coli genome. Mol Microbiol 1998, 29: 1341\u20131355. 10.1046\/j.1365-2958.1998.01008.x","journal-title":"Mol Microbiol"},{"key":"2314_CR18","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1007\/PL00006158","volume":"44","author":"JG Lawrence","year":"1997","unstructured":"Lawrence JG, Ochman H: Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44: 383\u2013397. 10.1007\/PL00006158","journal-title":"J Mol Evol"},{"key":"2314_CR19","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1016\/S0959-437X(00)00244-6","volume":"11","author":"MA Ragan","year":"2001","unstructured":"Ragan MA: Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev 2001, 11: 620\u2013626. 10.1016\/S0959-437X(00)00244-6","journal-title":"Curr Opin Genet Dev"},{"key":"2314_CR20","doi-asserted-by":"publisher","first-page":"3134","DOI":"10.1073\/pnas.95.6.3134","volume":"95","author":"DK Karaolis","year":"1998","unstructured":"Karaolis DK, Johnson JA, Bailey CC, Boedeker EC, Kaper JB, Reeves PR: A Vibrio cholerae pathogenicity island associated with epidemic and pandemic strains. Proc Natl Acad Sci U S A 1998, 95: 3134\u20133139. 10.1073\/pnas.95.6.3134","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2314_CR21","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1093\/dnares\/8.1.11","volume":"8","author":"T Hayashi","year":"2001","unstructured":"Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, Iida T, Takami H, Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, Shinagawa H: Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 2001, 8: 11\u201322. 10.1093\/dnares\/8.1.11","journal-title":"DNA Res"},{"key":"2314_CR22","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/35101614","volume":"413","author":"M McClelland","year":"2001","unstructured":"McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK: Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 2001, 413: 852\u2013856. 10.1038\/35101614","journal-title":"Nature"},{"key":"2314_CR23","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1038\/35101607","volume":"413","author":"J Parkhill","year":"2001","unstructured":"Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG: Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 2001, 413: 848\u2013852. 10.1038\/35101607","journal-title":"Nature"},{"key":"2314_CR24","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1038\/35054089","volume":"409","author":"NT Perna","year":"2001","unstructured":"Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR: Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 2001, 409: 529\u2013533. 10.1038\/35054089","journal-title":"Nature"},{"key":"2314_CR25","doi-asserted-by":"publisher","first-page":"10078","DOI":"10.1073\/pnas.152298499","volume":"99","author":"SB Beres","year":"2002","unstructured":"Beres SB, Sylva GL, Barbian KD, Lei B, Hoff JS, Mammarella ND, Liu MY, Smoot JC, Porcella SF, Parkins LD, Campbell DS, Smith TM, McCormick JK, Leung DY, Schlievert PM, Musser JM: Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc Natl Acad Sci U S A 2002, 99: 10078\u201310083. 10.1073\/pnas.152298499","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2314_CR26","doi-asserted-by":"publisher","first-page":"W97","DOI":"10.1093\/nar\/gkm380","volume":"35","author":"HY Ou","year":"2007","unstructured":"Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JC, Barer MR, Deng Z, Rajakumar K: MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res 2007, 35: W97-W104. 10.1093\/nar\/gkm380","journal-title":"Nucleic Acids Res"},{"key":"2314_CR27","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1186\/1471-2105-6-171","volume":"6","author":"H Chiapello","year":"2005","unstructured":"Chiapello H, Bourgait I, Sourivong F, Heuclin G, Gendrault-Jacquemard A, Petit MA, El Karoui M: Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinformatics 2005, 6: 171. 10.1186\/1471-2105-6-171","journal-title":"BMC Bioinformatics"},{"key":"2314_CR28","doi-asserted-by":"publisher","first-page":"4629","DOI":"10.1093\/nar\/gkm204","volume":"35","author":"RK Azad","year":"2007","unstructured":"Azad RK, Lawrence JG: Detecting laterally transferred genes: use of entropic clustering methods and genome position. Nucleic Acids Res 2007, 35: 4629\u20134639. 10.1093\/nar\/gkm204","journal-title":"Nucleic Acids Res"},{"key":"2314_CR29","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/1471-2105-7-142","volume":"7","author":"S Waack","year":"2006","unstructured":"Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R: Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006, 7: 142. 10.1186\/1471-2105-7-142","journal-title":"BMC Bioinformatics"},{"key":"2314_CR30","doi-asserted-by":"publisher","first-page":"R100","DOI":"10.1186\/gb-2007-8-6-r100","volume":"8","author":"GS Vernikos","year":"2007","unstructured":"Vernikos GS, Thomson NR, Parkhill J: Genetic flux over time in the Salmonella lineage. Genome Biol 2007, 8: R100. 10.1186\/gb-2007-8-6-r100","journal-title":"Genome Biol"},{"key":"2314_CR31","doi-asserted-by":"publisher","first-page":"1036","DOI":"10.1101\/gr.2231904","volume":"14","author":"V Daubin","year":"2004","unstructured":"Daubin V, Ochman H: Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli . Genome Res 2004, 14: 1036\u20131042. 10.1101\/gr.2231904","journal-title":"Genome Res"},{"key":"2314_CR32","unstructured":"National Center for Biotechnology Information (NCBI) FTP server[ftp:\/\/ftp.ncbi.nih.gov\/genomes\/Bacteria]"},{"key":"2314_CR33","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1093\/nar\/gkh362","volume":"32","author":"J Qi","year":"2004","unstructured":"Qi J, Luo H, Hao B: CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Research 2004, 32: 45\u201347. 10.1093\/nar\/gkh362","journal-title":"Nucleic Acids Research"},{"key":"2314_CR34","unstructured":"PHYLIP[http:\/\/evolution.genetics.washington.edu\/phylip.html]"},{"key":"2314_CR35","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1093\/oxfordjournals.molbev.a025665","volume":"13","author":"FS Lawson","year":"1996","unstructured":"Lawson FS, Charlebois RL, Dillon JA: Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life. Mol Biol Evol 1996, 13: 970\u2013977.","journal-title":"Mol Biol Evol"},{"key":"2314_CR36","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/S0168-9525(01)02597-5","volume":"18","author":"JO Korbel","year":"2002","unstructured":"Korbel JO, Snel B, Huynen MA, Bork P: SHOT: a web server for the construction of genome phylogenies. Trends in genetics : TIG 2002, 18: 158\u2013162. 10.1016\/S0168-9525(01)02597-5","journal-title":"Trends in genetics : TIG"},{"key":"2314_CR37","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","volume":"14","author":"ACE Darling","year":"2004","unstructured":"Darling ACE, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome research 2004, 14: 1394\u20131403. 10.1101\/gr.2289704","journal-title":"Genome research"},{"key":"2314_CR38","doi-asserted-by":"publisher","first-page":"D41","DOI":"10.1093\/nar\/gkj164","volume":"34","author":"JD Glasner","year":"2006","unstructured":"Glasner JD, Rusch M, Liss P, Plunkett G 3rd, Cabot EL, Darling A, Anderson BD, Infield-Harm P, Gilson MC, Perna NT: ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Res 2006, 34: D41\u20135. 10.1093\/nar\/gkj164","journal-title":"Nucleic Acids Res"},{"key":"2314_CR39","first-page":"322","volume":"2","author":"JM Greene","year":"2007","unstructured":"Greene JM, Perna N, Blattner F: ERIC-Comprehensive bioinformatics resources for enteropathogens. Microbe 2007, 2: 322\u2013323.","journal-title":"Microbe"},{"key":"2314_CR40","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. Nucleic Acids Res 1997, 25: 3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-329.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:00:08Z","timestamp":1630494008000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-329"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,8,5]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2314"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-329","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,8,5]]},"assertion":[{"value":"29 March 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 August 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 August 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"329"}}