{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T12:50:04Z","timestamp":1744203004559},"reference-count":50,"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>MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing between the 5'-end of miRNA and the target mRNA 3'-UTRs is essential for the miRNA:mRNA recognition. Recent studies show that many seed matches in 3'-UTRs, which are fully complementary to miRNA 5'-ends, are highly conserved. Based on these features, a two-stage strategy can be implemented to achieve the <jats:italic>de novo<\/jats:italic> identification of miRNAs by requiring the complete base-pairing between the 5'-end of miRNA candidates and the potential seed matches in 3'-UTRs.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We presented a new method, which combined multiple pairwise conservation information, to identify the frequently-occurred and conserved 7-mers in 3'-UTRs. A pairwise conservation score (PCS) was introduced to describe the conservation of all 7-mers in 3'-UTRs between any two <jats:italic>Drosophila<\/jats:italic> species. Using PCSs computed from 6 pairs of flies, we developed a support vector machine (SVM) classifier ensemble, named Cons-SVM and identified 689 conserved 7-mers including 63 seed matches covering 32 out of 38 known miRNA families in the reference dataset. In the second stage, we searched for 90 nt conserved stem-loop regions containing the complementary sequences to the identified 7-mers and used the previously published miRNA prediction software to analyze these stem-loops. We predicted 47 miRNA candidates in the genome-wide screen.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Cons-SVM takes advantage of the independent evolutionary information from the 6 pairs of flies and shows high sensitivity in identifying seed matches in 3'-UTRs. Combining the multiple pairwise conservation information by the machine learning approach, we finally identified 47 miRNA candidates in <jats:italic>D. melanogaster<\/jats:italic>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-432","type":"journal-article","created":{"date-parts":[[2007,11,8]],"date-time":"2007-11-08T19:13:30Z","timestamp":1194549210000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila"],"prefix":"10.1186","volume":"8","author":[{"given":"Jin","family":"Gu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hu","family":"Fu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuegong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanda","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,11,8]]},"reference":[{"issue":"2","key":"1804_CR1","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","volume":"116","author":"DP Bartel","year":"2004","unstructured":"Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281\u2013297. 10.1016\/S0092-8674(04)00045-5","journal-title":"Cell"},{"issue":"7006","key":"1804_CR2","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1038\/nature02871","volume":"431","author":"V Ambros","year":"2004","unstructured":"Ambros V: The functions of animal microRNAs. Nature 2004, 431(7006):350\u2013355. 10.1038\/nature02871","journal-title":"Nature"},{"issue":"5543","key":"1804_CR3","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1126\/science.1064921","volume":"294","author":"M Lagos-Quintana","year":"2001","unstructured":"Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T: Identification of novel genes coding for small expressed RNAs. Science 2001, 294(5543):853\u2013858. 10.1126\/science.1064921","journal-title":"Science"},{"issue":"2","key":"1804_CR4","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/S1534-5807(03)00228-4","volume":"5","author":"AA Aravin","year":"2003","unstructured":"Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T: The small RNA profile during Drosophila melanogaster development. Dev Cell 2003, 5(2):337\u2013350. 10.1016\/S1534-5807(03)00228-4","journal-title":"Dev Cell"},{"issue":"7","key":"1804_CR5","doi-asserted-by":"publisher","first-page":"R42","DOI":"10.1186\/gb-2003-4-7-r42","volume":"4","author":"EC Lai","year":"2003","unstructured":"Lai EC, Tomancak P, Williams RW, Rubin GM: Computational identification of Drosophila microRNA genes. Genome Biol 2003, 4(7):R42. 10.1186\/gb-2003-4-7-r42","journal-title":"Genome Biol"},{"issue":"6","key":"1804_CR6","doi-asserted-by":"publisher","first-page":"1193","DOI":"10.1016\/j.cell.2006.10.040","volume":"127","author":"JR Ruby","year":"2006","unstructured":"Ruby JR, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP: Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 2006, 127(6):1193\u20131207. 10.1016\/j.cell.2006.10.040","journal-title":"Cell"},{"issue":"1","key":"1804_CR7","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/j.cell.2004.12.031","volume":"120","author":"E Berezikov","year":"2005","unstructured":"Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E: Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005, 120(1):21\u201324. 10.1016\/j.cell.2004.12.031","journal-title":"Cell"},{"issue":"8","key":"1804_CR8","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1101\/gad.1074403","volume":"17","author":"LP Lim","year":"2003","unstructured":"Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP: The microRNAs of Caenorhabditis elegans. Genes Dev 2003, 17(8):991\u20131008. 10.1101\/gad.1074403","journal-title":"Genes Dev"},{"issue":"11","key":"1804_CR9","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1038\/nbt1144","volume":"23","author":"S Washietl","year":"2005","unstructured":"Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol 2005, 23(11):1383\u20131390. 10.1038\/nbt1144","journal-title":"Nat Biotechnol"},{"issue":"11","key":"1804_CR10","doi-asserted-by":"publisher","first-page":"3570","DOI":"10.1093\/nar\/gki668","volume":"33","author":"JW Nam","year":"2005","unstructured":"Nam JW, Shin KR, Han J, Lee Y, Kim VN, Zhang BT: Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res 2005, 33(11):3570\u20133581. 10.1093\/nar\/gki668","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"1804_CR11","doi-asserted-by":"publisher","first-page":"3610","DOI":"10.1093\/bioinformatics\/bti562","volume":"21","author":"X Wang","year":"2005","unstructured":"Wang X, Zhang J, Li F, Gu J, He T, Zhang X, Li Y: MicroRNA identification based on sequence and structure alignment. Bioinformatics 2005, 21(18):3610\u20133614. 10.1093\/bioinformatics\/bti562","journal-title":"Bioinformatics"},{"issue":"1","key":"1804_CR12","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1186\/1471-2105-6-310","volume":"6","author":"C Xue","year":"2005","unstructured":"Xue C, Li F, He T, Liu GP, Li Y, Zhang X: Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics 2005, 6(1):310. 10.1186\/1471-2105-6-310","journal-title":"BMC Bioinformatics"},{"key":"1804_CR13","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1186\/1471-2105-6-267","volume":"6","author":"A Sewer","year":"2005","unstructured":"Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M: Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 2005, 6: 267. 10.1186\/1471-2105-6-267","journal-title":"BMC Bioinformatics"},{"issue":"14","key":"1804_CR14","doi-asserted-by":"publisher","first-page":"e197","DOI":"10.1093\/bioinformatics\/btl257","volume":"22","author":"J Hertel","year":"2006","unstructured":"Hertel J, Stadler PF: Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics 2006, 22(14):e197-e202. 10.1093\/bioinformatics\/btl257","journal-title":"Bioinformatics"},{"issue":"1","key":"1804_CR15","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.cell.2004.12.035","volume":"120","author":"BP Lewis","year":"2005","unstructured":"Lewis BP, Burge CB, Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120(1):15\u201320. 10.1016\/j.cell.2004.12.035","journal-title":"Cell"},{"issue":"1","key":"1804_CR16","doi-asserted-by":"publisher","first-page":"e13","DOI":"10.1371\/journal.pcbi.0010013","volume":"1","author":"D Grun","year":"2005","unstructured":"Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N: microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 2005, 1(1):e13. 10.1371\/journal.pcbi.0010013","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"1804_CR17","doi-asserted-by":"publisher","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","volume":"5","author":"AJ Enright","year":"2003","unstructured":"Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS: MicroRNA targets in Drosophila. Genome Biol 2003, 5(1):R1. 10.1186\/gb-2003-5-1-r1","journal-title":"Genome Biol"},{"issue":"7","key":"1804_CR18","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/S0092-8674(03)01018-3","volume":"115","author":"BP Lewis","year":"2003","unstructured":"Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB: Prediction of mammalian microRNA targets. Cell 2003, 115(7):787\u2013798. 10.1016\/S0092-8674(03)01018-3","journal-title":"Cell"},{"issue":"5","key":"1804_CR19","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/ng1536","volume":"37","author":"A Krek","year":"2005","unstructured":"Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al.: Combinatorial microRNA target predictions. Nat Genet 2005, 37(5):495\u2013500. 10.1038\/ng1536","journal-title":"Nat Genet"},{"issue":"4","key":"1804_CR20","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/ng865","volume":"30","author":"EC Lai","year":"2002","unstructured":"Lai EC: Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 2002, 30(4):363\u2013364. 10.1038\/ng865","journal-title":"Nat Genet"},{"issue":"3","key":"1804_CR21","doi-asserted-by":"publisher","first-page":"E60","DOI":"10.1371\/journal.pbio.0000060","volume":"1","author":"A Stark","year":"2003","unstructured":"Stark A, Brennecke J, Russell RB, Cohen SM: Identification of Drosophila MicroRNA targets. PLoS Biol 2003, 1(3):E60. 10.1371\/journal.pbio.0000060","journal-title":"PLoS Biol"},{"issue":"3","key":"1804_CR22","doi-asserted-by":"publisher","first-page":"e85","DOI":"10.1371\/journal.pbio.0030085","volume":"3","author":"J Brennecke","year":"2005","unstructured":"Brennecke J, Stark A, Russell RB, Cohen SM: Principles of microRNA-target recognition. PLoS Biol 2005, 3(3):e85. 10.1371\/journal.pbio.0030085","journal-title":"PLoS Biol"},{"issue":"7031","key":"1804_CR23","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nature03441","volume":"434","author":"X Xie","year":"2005","unstructured":"Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M: Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 2005, 434(7031):338\u2013345. 10.1038\/nature03441","journal-title":"Nature"},{"issue":"7","key":"1804_CR24","doi-asserted-by":"publisher","first-page":"e69","DOI":"10.1371\/journal.pcbi.0010069","volume":"1","author":"CS Chan","year":"2005","unstructured":"Chan CS, Elemento O, Tavazoie S: Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation. PLoS Comput Biol 2005, 1(7):e69. 10.1371\/journal.pcbi.0010069","journal-title":"PLoS Comput Biol"},{"key":"1804_CR25","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1186\/1471-2105-5-170","volume":"5","author":"S Sinha","year":"2004","unstructured":"Sinha S, Blanchette M, Tompa M: PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 2004, 5: 170. 10.1186\/1471-2105-5-170","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"1804_CR26","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1101\/gr.3859605","volume":"15","author":"J Gertz","year":"2005","unstructured":"Gertz J, Riles L, Turnbaugh P, Ho SW, Cohen BA: Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics. Genome Res 2005, 15(8):1145\u20131152. 10.1101\/gr.3859605","journal-title":"Genome Res"},{"issue":"5","key":"1804_CR27","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1101\/gr.225502. Article published online before print in April 2002","volume":"12","author":"GG Loots","year":"2002","unstructured":"Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM: rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 2002, 12(5):832\u2013839. 10.1101\/gr.225502. Article published online before print in April 2002","journal-title":"Genome Res"},{"issue":"5611","key":"1804_CR28","doi-asserted-by":"publisher","first-page":"1391","DOI":"10.1126\/science.1081331","volume":"299","author":"D Boffelli","year":"2003","unstructured":"Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM: Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2003, 299(5611):1391\u20131394. 10.1126\/science.1081331","journal-title":"Science"},{"issue":"5629","key":"1804_CR29","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1126\/science.1084337","volume":"301","author":"P Cliften","year":"2003","unstructured":"Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M: Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 2003, 301(5629):71\u201376. 10.1126\/science.1084337","journal-title":"Science"},{"issue":"8","key":"1804_CR30","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1101\/gr.3715005","volume":"15","author":"A Siepel","year":"2005","unstructured":"Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al.: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15(8):1034\u20131050. 10.1101\/gr.3715005","journal-title":"Genome Res"},{"issue":"2","key":"1804_CR31","doi-asserted-by":"publisher","first-page":"R18","DOI":"10.1186\/gb-2005-6-2-r18","volume":"6","author":"O Elemento","year":"2005","unstructured":"Elemento O, Tavazoie S: Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol 2005, 6(2):R18. 10.1186\/gb-2005-6-2-r18","journal-title":"Genome Biol"},{"issue":"7043","key":"1804_CR32","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1038\/nature03552","volume":"435","author":"L He","year":"2005","unstructured":"He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, Hammond SM: A microRNA polycistron as a potential human oncogene. Nature 2005, 435(7043):828\u2013833. 10.1038\/nature03552","journal-title":"Nature"},{"issue":"21","key":"1804_CR33","doi-asserted-by":"publisher","first-page":"9628","DOI":"10.1158\/0008-5472.CAN-05-2352","volume":"65","author":"Y Hayashita","year":"2005","unstructured":"Hayashita Y, Osada H, Tatematsu Y, Yamada H, Yanagisawa K, Tomida S, Yatabe Y, Kawahara K, Sekido Y, Takahashi T: A polycistronic microRNA cluster, miR-17\u201392, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 2005, 65(21):9628\u20139632. 10.1158\/0008-5472.CAN-05-2352","journal-title":"Cancer Res"},{"issue":"5543","key":"1804_CR34","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1126\/science.1065062","volume":"294","author":"NC Lau","year":"2001","unstructured":"Lau NC, Lim LP, Weinstein EG, Bartel DP: An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001, 294(5543):858\u2013862. 10.1126\/science.1065062","journal-title":"Science"},{"key":"1804_CR35","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1093\/bioinformatics\/btg114","volume":"19","author":"CI Castillo-Davis","year":"2003","unstructured":"Castillo-Davis CI, Hartl DL: GeneMerge-postgenomic analysis, datamining, and hypothesis testing. Bioinformatics 2003, 19: 891\u2013892. 10.1093\/bioinformatics\/btg114","journal-title":"Bioinformatics"},{"key":"1804_CR36","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25\u201329. 10.1038\/75556","journal-title":"Nat Genet"},{"key":"1804_CR37","volume-title":"The Gene Ontology Annotation (GOA) Database","author":"E Camon","year":"2004","unstructured":"Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R: The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 2004, (32 Database):D262-D266. 10.1093\/nar\/gkh021"},{"issue":"Database issue","key":"1804_CR38","first-page":"D322","volume":"34","author":"Gene Ontology Consortium","year":"2004","unstructured":"Gene Ontology Consortium: The Gene Ontology(GO) project in 2006. Nucleic Acids Res 2004, 34(Database issue):D322-D326.","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"1804_CR39","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1016\/j.cell.2005.11.023","volume":"123","author":"A Stark","year":"2005","unstructured":"Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM: Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 2005, 123(6):1133\u20131146. 10.1016\/j.cell.2005.11.023","journal-title":"Cell"},{"issue":"1","key":"1804_CR40","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1093\/nar\/gkg129","volume":"31","author":"D Karolchik","year":"2003","unstructured":"Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, et al.: The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31(1):51\u201354. 10.1093\/nar\/gkg129","journal-title":"Nucleic Acids Res"},{"key":"1804_CR41","volume-title":"The UCSC Genome Browser Database","author":"AS Hinrichs","year":"2006","unstructured":"Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, et al.: The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 2006, (34 Database):D590\u2013598. 10.1093\/nar\/gkj144"},{"key":"1804_CR42","unstructured":"Clote P: The Altschul-Erikson algorithm.[http:\/\/bioinformatics.bc.edu\/clotelab\/RNAdinucleotideShuffle\/dinucleotideShuffle.html]"},{"key":"1804_CR43","unstructured":"Washietl S: Alifoldz algorithm.[http:\/\/www.tbi.univie.ac.at\/papers\/SUPPLEMENTS\/Alifoldz\/]"},{"key":"1804_CR44","volume-title":"miRBase","author":"S Griffiths-Jones","year":"2006","unstructured":"Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ: miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, (34 Database):D140\u2013144. 10.1093\/nar\/gkj112"},{"key":"1804_CR45","unstructured":"Gu J: The pairwise conservation score program.[http:\/\/bioinfo.au.tsinghua.edu.cn\/member\/~gujin\/pcs\/]"},{"key":"1804_CR46","first-page":"752","volume-title":"The Twentieth International Conference on Machine Learning, ICML","author":"G Valentini","year":"2003","unstructured":"Valentini G, Dietterich TG: Low Bias Bagged Support Vector Machines. The Twentieth International Conference on Machine Learning, ICML 2003, 752\u2013759."},{"key":"1804_CR47","unstructured":"Chang C, Lin C: LIBSVM: a library for support vector machines.[http:\/\/www.csie.ntu.edu.tw\/~cjlin\/libsvm]"},{"key":"1804_CR48","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/BF00818163","volume":"125","author":"IL Hofacker","year":"1994","unstructured":"Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P: Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f Chemie 1994, 125: 167\u2013188. 10.1007\/BF00818163","journal-title":"Monatshefte f Chemie"},{"key":"1804_CR49","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1101\/gr.849004","volume":"14","author":"GE Crooks","year":"2004","unstructured":"Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: A sequence logo generator. Genome Res 2004, 14: 1188\u20131190. 10.1101\/gr.849004","journal-title":"Genome Res"},{"issue":"17","key":"1804_CR50","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(17):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\/1471-2105-8-432.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T10:17:28Z","timestamp":1630491448000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-432"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,11,8]]},"references-count":50,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1804"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-432","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,11,8]]},"assertion":[{"value":"21 November 2006","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"432"}}