{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T02:13:25Z","timestamp":1773022405026,"version":"3.50.1"},"reference-count":35,"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 recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hundreds of miRNAs have been identified by direct cloning and computational approaches in several species. However, there are still many miRNAs that remain to be identified due to lack of either sequence features or robust algorithms to efficiently identify them.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have evaluated features valuable for pre-miRNA prediction, such as the local secondary structure differences of the stem region of miRNA and non-miRNA hairpins. We have also established correlations between different types of mutations and the secondary structures of pre-miRNAs. Utilizing these features and combining some improvements of the current pre-miRNA prediction methods, we implemented a computational learning method SVM (support vector machine) to build a high throughput and good performance computational pre-miRNA prediction tool called MiRFinder. The tool was designed for genome-wise, pair-wise sequences from two related species. The method built into the tool consisted of two major steps: 1) genome wide search for hairpin candidates and 2) exclusion of the non-robust structures based on analysis of 18 parameters by the SVM method. Results from applying the tool for chicken\/human and D. melanogaster\/D. pseudoobscura pair-wise genome alignments showed that the tool can be used for genome wide pre-miRNA predictions.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The MiRFinder can be a good alternative to current miRNA discovery software. This tool is available at <jats:ext-link xmlns:xlink=\"https:\/\/2.zoppoz.workers.dev:443\/http\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/2.zoppoz.workers.dev:443\/http\/www.bioinformatics.org\/mirfinder\/\" ext-link-type=\"uri\">https:\/\/2.zoppoz.workers.dev:443\/http\/www.bioinformatics.org\/mirfinder\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-341","type":"journal-article","created":{"date-parts":[[2007,9,18]],"date-time":"2007-09-18T06:13:29Z","timestamp":1190096009000},"update-policy":"https:\/\/2.zoppoz.workers.dev:443\/https\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":123,"title":["MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans"],"prefix":"10.1186","volume":"8","author":[{"given":"Ting-Hua","family":"Huang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Fan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Max F","family":"Rothschild","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhi-Liang","family":"Hu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kui","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shu-Hong","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,9,17]]},"reference":[{"issue":"20","key":"1713_CR1","doi-asserted-by":"publisher","first-page":"4051","DOI":"10.1038\/sj.emboj.7600385","volume":"23","author":"Y Lee","year":"2004","unstructured":"Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN: MicroRNA genes are transcribed by RNA polymerase II. Embo J 2004, 23(20):4051\u20134060. 10.1038\/sj.emboj.7600385","journal-title":"Embo J"},{"issue":"12","key":"1713_CR2","doi-asserted-by":"publisher","first-page":"1957","DOI":"10.1261\/rna.7135204","volume":"10","author":"X Cai","year":"2004","unstructured":"Cai X, Hagedorn CH, Cullen BR: Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. Rna 2004, 10(12):1957\u20131966. 10.1261\/rna.7135204","journal-title":"Rna"},{"issue":"6956","key":"1713_CR3","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature01957","volume":"425","author":"Y Lee","year":"2003","unstructured":"Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN: The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425(6956):415\u2013419. 10.1038\/nature01957","journal-title":"Nature"},{"issue":"5654","key":"1713_CR4","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1126\/science.1090599","volume":"303","author":"E Lund","year":"2004","unstructured":"Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U: Nuclear export of microRNA precursors. Science 2004, 303(5654):95\u201398. 10.1126\/science.1090599","journal-title":"Science"},{"issue":"24","key":"1713_CR5","doi-asserted-by":"publisher","first-page":"3011","DOI":"10.1101\/gad.1158803","volume":"17","author":"R Yi","year":"2003","unstructured":"Yi R, Qin Y, Macara IG, Cullen BR: Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes & development 2003, 17(24):3011\u20133016. 10.1101\/gad.1158803","journal-title":"Genes & development"},{"issue":"2","key":"1713_CR6","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1261\/rna.5167604","volume":"10","author":"MT Bohnsack","year":"2004","unstructured":"Bohnsack MT, Czaplinski K, Gorlich D: Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. Rna 2004, 10(2):185\u2013191. 10.1261\/rna.5167604","journal-title":"Rna"},{"issue":"8","key":"1713_CR7","doi-asserted-by":"publisher","first-page":"5505","DOI":"10.1074\/jbc.C200668200","volume":"278","author":"C Gwizdek","year":"2003","unstructured":"Gwizdek C, Ossareh-Nazari B, Brownawell AM, Doglio A, Bertrand E, Macara IG, Dargemont C: Exportin-5 mediates nuclear export of minihelix-containing RNAs. J Biol Chem 2003, 278(8):5505\u20135508. 10.1074\/jbc.C200668200","journal-title":"J Biol Chem"},{"issue":"5531","key":"1713_CR8","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1126\/science.1062961","volume":"293","author":"G Hutvagner","year":"2001","unstructured":"Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD: A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 2001, 293(5531):834\u2013838. 10.1126\/science.1062961","journal-title":"Science"},{"issue":"20","key":"1713_CR9","doi-asserted-by":"publisher","first-page":"2654","DOI":"10.1101\/gad.927801","volume":"15","author":"RF Ketting","year":"2001","unstructured":"Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, Plasterk RH: Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 2001, 15(20):2654\u20132659. 10.1101\/gad.927801","journal-title":"Genes Dev"},{"issue":"5538","key":"1713_CR10","doi-asserted-by":"publisher","first-page":"2269","DOI":"10.1126\/science.1062039","volume":"293","author":"SW Knight","year":"2001","unstructured":"Knight SW, Bass BL: A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 2001, 293(5538):2269\u20132271. 10.1126\/science.1062039","journal-title":"Science"},{"issue":"2","key":"1713_CR11","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1002\/bies.10046","volume":"24","author":"D Banerjee","year":"2002","unstructured":"Banerjee D, Slack F: Control of developmental timing by small temporal RNAs: a paradigm for RNA-mediated regulation of gene expression. Bioessays 2002, 24(2):119\u2013129. 10.1002\/bies.10046","journal-title":"Bioessays"},{"issue":"5543","key":"1713_CR12","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":"5543","key":"1713_CR13","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1126\/science.1065329","volume":"294","author":"RC Lee","year":"2001","unstructured":"Lee RC, Ambros V: An extensive class of small RNAs in Caenorhabditis elegans. Science 2001, 294(5543):862\u2013864. 10.1126\/science.1065329","journal-title":"Science"},{"issue":"5543","key":"1713_CR14","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"},{"issue":"18","key":"1713_CR15","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 (Oxford, England) 2005, 21(18):3610\u20133614. 10.1093\/bioinformatics\/bti562","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"7","key":"1713_CR16","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":"31","key":"1713_CR17","doi-asserted-by":"publisher","first-page":"11511","DOI":"10.1073\/pnas.0404025101","volume":"101","author":"E Bonnet","year":"2004","unstructured":"Bonnet E, Wuyts J, Rouze P, Van de Peer Y: Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 2004, 101(31):11511\u201311516. 10.1073\/pnas.0404025101","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6","key":"1713_CR18","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/j.molcel.2004.05.027","volume":"14","author":"MW Jones-Rhoades","year":"2004","unstructured":"Jones-Rhoades MW, Bartel DP: Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004, 14(6):787\u2013799. 10.1016\/j.molcel.2004.05.027","journal-title":"Mol Cell"},{"issue":"11","key":"1713_CR19","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"},{"key":"1713_CR20","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"},{"key":"1713_CR21","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: 310. 10.1186\/1471-2105-6-310","journal-title":"BMC bioinformatics"},{"issue":"4","key":"1713_CR22","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1038\/nmeth746","volume":"2","author":"S Pfeffer","year":"2005","unstructured":"Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T: Identification of microRNAs of the herpesvirus family. Nature methods 2005, 2(4):269\u2013276. 10.1038\/nmeth746","journal-title":"Nature methods"},{"issue":"14","key":"1713_CR23","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 (Oxford, England) 2006, 22(14):e197\u2013202. 10.1093\/bioinformatics\/btl257","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"2","key":"1713_CR24","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1093\/bioinformatics\/btl570","volume":"23","author":"SA Helvik","year":"2007","unstructured":"Helvik SA, Snove O Jr, Saetrom P: Reliable prediction of Drosha processing sites improves microRNA gene prediction. Bioinformatics (Oxford, England) 2007, 23(2):142\u2013149. 10.1093\/bioinformatics\/btl570","journal-title":"Bioinformatics (Oxford, England)"},{"key":"1713_CR25","volume-title":"Bioinformatics (Oxford, England)","author":"SN Kwang Loong","year":"2007","unstructured":"Kwang Loong SN, Mishra SK: De Novo SVM Classification of Precursor MicroRNAs from Genomic Pseudo Hairpins Using Global and Intrinsic Folding Measures. Bioinformatics (Oxford, England) 2007."},{"issue":"3","key":"1713_CR26","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/j.tig.2006.01.003","volume":"22","author":"VN Kim","year":"2006","unstructured":"Kim VN, Nam JW: Genomics of microRNA. Trends Genet 2006, 22(3):165\u2013173. 10.1016\/j.tig.2006.01.003","journal-title":"Trends Genet"},{"issue":"1","key":"1713_CR27","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":"7","key":"1713_CR28","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1093\/bioinformatics\/bti132","volume":"21","author":"G Dror","year":"2005","unstructured":"Dror G, Sorek R, Shamir R: Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics (Oxford, England) 2005, 21(7):897\u2013901. 10.1093\/bioinformatics\/bti132","journal-title":"Bioinformatics (Oxford, England)"},{"key":"1713_CR29","first-page":"D140","volume-title":"Nucleic Acids Res","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":"1713_CR30","first-page":"D590","volume-title":"Nucleic Acids Res","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"},{"issue":"1","key":"1713_CR31","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/nbt1053","volume":"23","author":"M Tompa","year":"2005","unstructured":"Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, et al.: Assessing computational tools for the discovery of transcription factor binding sites. Nature biotechnology 2005, 23(1):137\u2013144. 10.1038\/nbt1053","journal-title":"Nature biotechnology"},{"issue":"1","key":"1713_CR32","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981, 147(1):195\u2013197. 10.1016\/0022-2836(81)90087-5","journal-title":"J Mol Biol"},{"issue":"5","key":"1713_CR33","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","volume":"288","author":"DH Mathews","year":"1999","unstructured":"Mathews DH, Sabina J, Zuker M, Turner DH: Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999, 288(5):911\u2013940. 10.1006\/jmbi.1999.2700","journal-title":"J Mol Biol"},{"key":"1713_CR34","volume-title":"LIBSVM: a library for support vector machines","author":"C-C Chang","year":"2001","unstructured":"Chang C-C, Lin C-J: LIBSVM: a library for support vector machines. 2001."},{"issue":"8","key":"1713_CR35","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"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-341.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T01:54:55Z","timestamp":1630461295000},"score":1,"resource":{"primary":{"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-341"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,9,17]]},"references-count":35,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1713"],"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/doi.org\/10.1186\/1471-2105-8-341","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,9,17]]},"assertion":[{"value":"13 February 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 September 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 September 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"341"}}