{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T22:33:58Z","timestamp":1778193238450,"version":"3.51.4"},"reference-count":86,"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":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, computational methods that can accurately detect ncRNAs in sequenced genomes are therefore desirable. The increasing number of genomic sequences provides a rich dataset for computational comparative sequence analysis and detection of novel ncRNAs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here, Dynalign, a program for predicting secondary structures common to two RNA sequences on the basis of minimizing folding free energy change, is utilized as a computational ncRNA detection tool. The Dynalign-computed optimal total free energy change, which scores the structural alignment and the free energy change of folding into a common structure for two RNA sequences, is shown to be an effective measure for distinguishing ncRNA from randomized sequences. To make the classification as a ncRNA, the total free energy change of an input sequence pair can either be compared with the total free energy changes of a set of control sequence pairs, or be used in combination with sequence length and nucleotide frequencies as input to a classification support vector machine. The latter method is much faster, but slightly less sensitive at a given specificity. Additionally, the classification support vector machine method is shown to be sensitive and specific on genomic ncRNA screens of two different\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      and\n                      <jats:italic>Salmonella typhi<\/jats:italic>\n                      genome alignments, in which many ncRNAs are known. The Dynalign computational experiments are also compared with two other ncRNA detection programs, RNAz and QRNA.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The Dynalign-based support vector machine method is more sensitive for known ncRNAs in the test genomic screens than RNAz and QRNA. Additionally, both Dynalign-based methods are more sensitive than RNAz and QRNA at low sequence pair identities. Dynalign can be used as a comparable or more accurate tool than RNAz or QRNA in genomic screens, especially for low-identity regions. Dynalign provides a method for discovering ncRNAs in sequenced genomes that other methods may not identify. Significant improvements in Dynalign runtime have also been achieved.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/1471-2105-7-173","type":"journal-article","created":{"date-parts":[[2006,4,6]],"date-time":"2006-04-06T08:50:36Z","timestamp":1144313436000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":150,"title":["Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change"],"prefix":"10.1186","volume":"7","author":[{"given":"Andrew V","family":"Uzilov","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joshua M","family":"Keegan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David H","family":"Mathews","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,3,27]]},"reference":[{"key":"912_CR1","doi-asserted-by":"publisher","first-page":"920","DOI":"10.1126\/science.289.5481.920","volume":"289","author":"P Nissen","year":"2000","unstructured":"Nissen P, Hansen J, Ban N, Moore PB, Steitz TA: The structural basis of ribosomal activity in peptide bond synthesis. Science 2000, 289: 920\u2013930. 10.1126\/science.289.5481.920","journal-title":"Science"},{"key":"912_CR2","doi-asserted-by":"publisher","first-page":"11670","DOI":"10.1073\/pnas.172404099","volume":"99","author":"JL Hansen","year":"2002","unstructured":"Hansen JL, Schmeing TM, Moore PB, Steitz TA: Structural insights into peptide bond formation. Proc Natl Acad Sci U S A 2002, 99: 11670\u201311675. 10.1073\/pnas.172404099","journal-title":"Proc Natl Acad Sci U S A"},{"key":"912_CR3","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1038\/299691a0","volume":"299","author":"P Walter","year":"1982","unstructured":"Walter P, Blobel G: Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature 1982, 299: 691\u2013698. 10.1038\/299691a0","journal-title":"Nature"},{"key":"912_CR4","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/ni0702-597","volume":"3","author":"BR Cullen","year":"2002","unstructured":"Cullen BR: RNA interference: antiviral defense and genetic tool. Nat Immunol 2002, 3: 597\u2013599. 10.1038\/ni0702-597","journal-title":"Nat Immunol"},{"key":"912_CR5","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/418222a","volume":"418","author":"JA Doudna","year":"2002","unstructured":"Doudna JA, Cech TR: The chemical repertoire of natural ribozymes. Nature 2002, 418: 222\u2013228. 10.1038\/418222a","journal-title":"Nature"},{"key":"912_CR6","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1016\/S0092-8674(00)81155-1","volume":"93","author":"B Panning","year":"1998","unstructured":"Panning B, Jaenisch R: RNA and the epigenetic regulation of X chromosome inactivation. Cell 1998, 93: 305\u2013308. 10.1016\/S0092-8674(00)81155-1","journal-title":"Cell"},{"key":"912_CR7","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1038\/79594","volume":"7","author":"EH Blackburn","year":"2000","unstructured":"Blackburn EH: The end of the (DNA) line. Nat Struct Biol 2000, 7: 847\u2013850. 10.1038\/79594","journal-title":"Nat Struct Biol"},{"key":"912_CR8","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1046\/j.1365-2958.2001.02381.x","volume":"40","author":"PP Dennis","year":"2001","unstructured":"Dennis PP, Omer A, Lowe T: A guided tour: small RNA function in Archaea. Mol Microbiol 2001, 40: 509\u2013519. 10.1046\/j.1365-2958.2001.02381.x","journal-title":"Mol Microbiol"},{"key":"912_CR9","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1016\/S0300-9084(02)01402-5","volume":"84","author":"JP Bachellerie","year":"2002","unstructured":"Bachellerie JP, Cavaille J, Huttenhofer A: The expanding snoRNA world. Biochimie 2002, 84: 775\u2013790. 10.1016\/S0300-9084(02)01402-5","journal-title":"Biochimie"},{"key":"912_CR10","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: 858\u2013862. 10.1126\/science.1065062","journal-title":"Science"},{"key":"912_CR11","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: 853\u2013858. 10.1126\/science.1064921","journal-title":"Science"},{"key":"912_CR12","doi-asserted-by":"publisher","first-page":"9736","DOI":"10.1073\/pnas.161168098","volume":"98","author":"J Miranda-Rios","year":"2001","unstructured":"Miranda-Rios J, Navarror M, Sober\u00f3n M: A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc Natl Acad Sci U S A 2001, 98: 9736\u20139741. 10.1073\/pnas.161168098","journal-title":"Proc Natl Acad Sci U S A"},{"key":"912_CR13","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1093\/nar\/gkg124","volume":"31","author":"M Szymanski","year":"2003","unstructured":"Szymanski M, Erdmann VA, Barciszewska J: Noncoding regulatory RNAs database. Nucleic Acids Res 2003, 31: 429\u2013431. 10.1093\/nar\/gkg124","journal-title":"Nucleic Acids Res"},{"key":"912_CR14","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1046\/j.1365-2958.2003.03459.x","volume":"48","author":"T Weilbacher","year":"2003","unstructured":"Weilbacher T, Suzuki K, Dubey AK, Wang X, Gudapaty S, Morozov I, Baker CS, Georgellis D, Babitzke P, Romeo T: A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol Microbiol 2003, 48: 657\u2013670. 10.1046\/j.1365-2958.2003.03459.x","journal-title":"Mol Microbiol"},{"key":"912_CR15","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1093\/nar\/gkg006","volume":"31","author":"S Griffiths-Jones","year":"2003","unstructured":"Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR: Rfam: an RNA family database. Nucleic Acids Res 2003, 31: 439\u2013441. 10.1093\/nar\/gkg006","journal-title":"Nucleic Acids Res"},{"key":"912_CR16","doi-asserted-by":"publisher","first-page":"D121","DOI":"10.1093\/nar\/gki081","volume":"33","author":"S Griffiths-Jones","year":"2005","unstructured":"Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A: Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005, 33: D121\u2013124. 10.1093\/nar\/gki081","journal-title":"Nucleic Acids Res"},{"key":"912_CR17","doi-asserted-by":"publisher","first-page":"D125","DOI":"10.1093\/nar\/gki089","volume":"33","author":"KC Pang","year":"2005","unstructured":"Pang KC, Stephen S, Engstr\u00f6m PG, Tajul-Arifin K, Chen W, Wahlestedt C, Lenhard B, Hayashizaki Y, Mattick JS: RNAdb \u2014 a comprehensive mammalian noncoding RNA database. Nucleic Acids Res 2005, 33: D125-D130. 10.1093\/nar\/gki089","journal-title":"Nucleic Acids Res"},{"key":"912_CR18","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1038\/35103511","volume":"2","author":"SR Eddy","year":"2001","unstructured":"Eddy SR: Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001, 2: 919\u2013929. 10.1038\/35103511","journal-title":"Nat Rev Genet"},{"key":"912_CR19","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1093\/bioinformatics\/16.7.583","volume":"16","author":"E Rivas","year":"2000","unstructured":"Rivas E, Eddy SR: Secondary structure alone is not statistically significant for the detection of noncoding RNAs. Bioinformatics 2000, 16: 583\u2013605. 10.1093\/bioinformatics\/16.7.583","journal-title":"Bioinformatics"},{"key":"912_CR20","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/S0092-8674(02)00717-1","volume":"109","author":"KM Wassarman","year":"2002","unstructured":"Wassarman KM: Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes. Cell 2002, 109: 141\u2013144. 10.1016\/S0092-8674(02)00717-1","journal-title":"Cell"},{"key":"912_CR21","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1038\/nsmb813","volume":"11","author":"TA Allen","year":"2004","unstructured":"Allen TA, Von Kaenel S, Goodrich JA, Kugel JF: The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol 2004, 11: 816\u2013821. 10.1038\/nsmb813","journal-title":"Nat Struct Mol Biol"},{"key":"912_CR22","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/S1097-2765(01)00437-3","volume":"9","author":"A Zhang","year":"2002","unstructured":"Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G: The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 2002, 9: 11\u201322. 10.1016\/S1097-2765(01)00437-3","journal-title":"Mol Cell"},{"key":"912_CR23","doi-asserted-by":"publisher","first-page":"2943","DOI":"10.1093\/emboj\/20.11.2943","volume":"20","author":"A H\u00fcttenhofer","year":"2001","unstructured":"H\u00fcttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H, Bachellerie JP, Brosius J: RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. Embo J 2001, 20: 2943\u20132953. 10.1093\/emboj\/20.11.2943","journal-title":"Embo J"},{"key":"912_CR24","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/nature01266","volume":"420","author":"Y Okazaki","year":"2002","unstructured":"Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y, FANTOM Consortium, RIKEN Genome Exploration Research Group Phase I & II Team: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420: 563\u2013573. 10.1038\/nature01266","journal-title":"Nature"},{"key":"912_CR25","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1016\/S0960-9822(01)00401-8","volume":"11","author":"E Rivas","year":"2001","unstructured":"Rivas E, Klein RJ, Jones TA, Eddy SR: Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 2001, 11: 1369\u20131373. 10.1016\/S0960-9822(01)00401-8","journal-title":"Curr Biol"},{"key":"912_CR26","doi-asserted-by":"publisher","first-page":"4119","DOI":"10.1093\/nar\/gkg438","volume":"31","author":"JP McCutcheon","year":"2003","unstructured":"McCutcheon JP, Eddy SR: Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res 2003, 31: 4119\u20134128. 10.1093\/nar\/gkg438","journal-title":"Nucleic Acids Res"},{"key":"912_CR27","doi-asserted-by":"publisher","first-page":"R73","DOI":"10.1186\/gb-2005-6-9-r73","volume":"6","author":"IM Axmann","year":"2005","unstructured":"Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR: Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol 2005, 6: R73. 10.1186\/gb-2005-6-9-r73","journal-title":"Genome Biol"},{"key":"912_CR28","doi-asserted-by":"publisher","first-page":"1637","DOI":"10.1101\/gad.901001","volume":"15","author":"KM Wassarman","year":"2001","unstructured":"Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S: Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 2001, 15: 1637\u20131651. 10.1101\/gad.901001","journal-title":"Genes Dev"},{"key":"912_CR29","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1016\/S0960-9822(01)00270-6","volume":"11","author":"L Argaman","year":"2001","unstructured":"Argaman L, Herschberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuva S: Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 2001, 11: 941\u2013950. 10.1016\/S0960-9822(01)00270-6","journal-title":"Curr Biol"},{"key":"912_CR30","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: 1383\u20131390. 10.1038\/nbt1144","journal-title":"Nat Biotechnol"},{"key":"912_CR31","doi-asserted-by":"publisher","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","volume":"277","author":"FR Blattner","year":"1997","unstructured":"Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science 1997, 277: 1453\u20131474. 10.1126\/science.277.5331.1453","journal-title":"Science"},{"key":"912_CR32","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":"912_CR33","doi-asserted-by":"publisher","first-page":"2012","DOI":"10.1126\/science.282.5396.2012","volume":"282","author":"C. elegans Sequencing Consortium","year":"1998","unstructured":"C. elegans Sequencing Consortium: Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998, 282: 2012\u20132018. 10.1126\/science.282.5396.2012","journal-title":"Science"},{"key":"912_CR34","doi-asserted-by":"publisher","first-page":"D311","DOI":"10.1093\/nar\/gkh033","volume":"32","author":"KR Christie","year":"2004","unstructured":"Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM: Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res 2004, 32: D311\u2013314. 10.1093\/nar\/gkh033","journal-title":"Nucleic Acids Res"},{"key":"912_CR35","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1146\/annurev.genom.4.070802.110323","volume":"4","author":"SE Celniker","year":"2003","unstructured":"Celniker SE, Rubin GM: The Drosophila melanogaster genome. Annu Rev Genomics Hum Genet 2003, 4: 89\u2013117. 10.1146\/annurev.genom.4.070802.110323","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"912_CR36","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1038\/nature01262","volume":"420","author":"Mouse Genome Sequencing Consortium","year":"2002","unstructured":"Mouse Genome Sequencing Consortium: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420: 520\u2013562. 10.1038\/nature01262","journal-title":"Nature"},{"key":"912_CR37","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1038\/nature03062","volume":"431","author":"International Human Genome Sequencing Consortium","year":"2004","unstructured":"International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome . Nature 2004, 431: 927\u2013930. 10.1038\/nature03062","journal-title":"Nature"},{"key":"912_CR38","first-page":"153","volume":"4","author":"SV Le","year":"1988","unstructured":"Le SV, Chen JH, Currey KM, Maizel JVJ: A program for predicting significant RNA secondary structures. Comput Appl Biosci 1988, 4: 153\u2013159.","journal-title":"Comput Appl Biosci"},{"key":"912_CR39","doi-asserted-by":"publisher","first-page":"6143","DOI":"10.1093\/nar\/17.15.6143","volume":"17","author":"SY Le","year":"1989","unstructured":"Le SY, Chen JH, Maizel JV: Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses. Nucleic Acids Res 1989, 17: 6143\u20136152.","journal-title":"Nucleic Acids Res"},{"key":"912_CR40","first-page":"7","volume":"6","author":"JH Chen","year":"1990","unstructured":"Chen JH, Le SY, Shapiro B, Currey KM, Maizel JV: A computational procedure for assessing the significance of RNA secondary structure. Comput Appl Biosci 1990, 6: 7\u201318.","journal-title":"Comput Appl Biosci"},{"key":"912_CR41","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1261\/rna.7220505","volume":"11","author":"P Clote","year":"2005","unstructured":"Clote P, Ferre F, Kranakis E, Krizanc D: Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 2005, 11: 578\u2013591. 10.1261\/rna.7220505","journal-title":"RNA"},{"key":"912_CR42","doi-asserted-by":"publisher","first-page":"4816","DOI":"10.1093\/nar\/27.24.4816","volume":"27","author":"C Workman","year":"1999","unstructured":"Workman C, Krogh A: No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res 1999, 27: 4816\u20134822. 10.1093\/nar\/27.24.4816","journal-title":"Nucleic Acids Res"},{"key":"912_CR43","doi-asserted-by":"publisher","first-page":"2454","DOI":"10.1073\/pnas.0409169102","volume":"102","author":"S Washietl","year":"2005","unstructured":"Washietl S, Hofacker IL, Stadler PF: Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A 2005, 102: 2454\u20132459. 10.1073\/pnas.0409169102","journal-title":"Proc Natl Acad Sci U S A"},{"key":"912_CR44","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.jmb.2004.07.018","volume":"342","author":"S Washietl","year":"2004","unstructured":"Washietl S, Hofacker IL: Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 2004, 342: 19\u201330. 10.1016\/j.jmb.2004.07.018","journal-title":"J Mol Biol"},{"key":"912_CR45","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1006\/jmbi.2001.5351","volume":"317","author":"DH Mathews","year":"2002","unstructured":"Mathews DH, Turner DH: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol 2002, 317: 191\u2013203. 10.1006\/jmbi.2001.5351","journal-title":"J Mol Biol"},{"key":"912_CR46","doi-asserted-by":"publisher","first-page":"2246","DOI":"10.1093\/bioinformatics\/bti349","volume":"21","author":"DH Mathews","year":"2005","unstructured":"Mathews DH: Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics 2005, 21: 2246\u20132253. 10.1093\/bioinformatics\/bti349","journal-title":"Bioinformatics"},{"key":"912_CR47","doi-asserted-by":"publisher","first-page":"14719","DOI":"10.1021\/bi9809425","volume":"37","author":"T Xia","year":"1998","unstructured":"Xia T, SantaLucia JJ, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH: Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry 1998, 37: 14719\u201314735. 10.1021\/bi9809425","journal-title":"Biochemistry"},{"key":"912_CR48","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 provides improved prediction of RNA secondary structure. J Mol Biol 1999, 288: 911\u2013940. 10.1006\/jmbi.1999.2700","journal-title":"J Mol Biol"},{"key":"912_CR49","doi-asserted-by":"publisher","first-page":"7287","DOI":"10.1073\/pnas.0401799101","volume":"101","author":"DH Mathews","year":"2004","unstructured":"Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH: Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 2004, 101: 7287\u20137292. 10.1073\/pnas.0401799101","journal-title":"Proc Natl Acad Sci USA"},{"key":"912_CR50","first-page":"91","volume-title":"The RNA World","author":"CR Woese","year":"1993","unstructured":"Woese CR, Pace NR: Probing RNA structure, function, and history by comparitive analysis. In The RNA World. Edited by: Gesteland RF, Atkins JF. New York, Cold Spring Harbor Press; 1993:91\u2013117."},{"key":"912_CR51","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/S0168-9525(00)88996-9","volume":"11","author":"T Dandekar","year":"1995","unstructured":"Dandekar T, Hentze MW: Finding the hairpin in the haystack: searching for RNA motifs. Trends Genet 1995, 11: 45\u201350. 10.1016\/S0168-9525(00)88996-9","journal-title":"Trends Genet"},{"key":"912_CR52","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","volume":"25","author":"TM Lowe","year":"1997","unstructured":"Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 1997, 25: 955\u2013964. 10.1093\/nar\/25.5.955","journal-title":"Nucl Acids Res"},{"key":"912_CR53","doi-asserted-by":"publisher","first-page":"1168","DOI":"10.1126\/science.283.5405.1168","volume":"283","author":"TM Lowe","year":"1999","unstructured":"Lowe TM, Eddy SR: A computational screen for methylation guide snoRNAs in yeast. Science 1999, 283: 1168\u20131171. 10.1126\/science.283.5405.1168","journal-title":"Science"},{"key":"912_CR54","doi-asserted-by":"publisher","first-page":"3368","DOI":"10.1093\/nar\/gkf468","volume":"30","author":"M Regalia","year":"2002","unstructured":"Regalia M, Rosenblad MA, Samuelsson T: Prediction of signal recognition particle RNA genes. Nucleic Acids Res 2002, 30: 3368\u20133377. 10.1093\/nar\/gkf468","journal-title":"Nucleic Acids Res"},{"key":"912_CR55","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: 991\u20131008. 10.1101\/gad.1074403","journal-title":"Genes Dev"},{"key":"912_CR56","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1093\/bioinformatics\/btg080","volume":"19","author":"S Edvardsson","year":"2003","unstructured":"Edvardsson S, Gardner PP, Poole AM, Hendy MD, Penny D, Moulton V: A search for H\/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics 2003, 19: 865\u2013873. 10.1093\/bioinformatics\/btg080","journal-title":"Bioinformatics"},{"key":"912_CR57","doi-asserted-by":"publisher","first-page":"4281","DOI":"10.1093\/nar\/gkh768","volume":"32","author":"P Schattner","year":"2004","unstructured":"Schattner P, Decatur WA, Davis CA, Ares MJ, Fournier MJ, Lowe TM: Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res 2004, 32: 4281\u20134296. 10.1093\/nar\/gkh768","journal-title":"Nucleic Acids Res"},{"key":"912_CR58","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/1471-2105-4-44","volume":"4","author":"RJ Klein","year":"2003","unstructured":"Klein RJ, Eddy SR: RSEARCH: finding homologs of single structures RNA sequences. BMC Bioinformatics 2003, 4: 44. 10.1186\/1471-2105-4-44","journal-title":"BMC Bioinformatics"},{"key":"912_CR59","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1471-2105-2-8","volume":"2","author":"E Rivas","year":"2001","unstructured":"Rivas E, Eddy SR: Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001, 2: 8. 10.1186\/1471-2105-2-8","journal-title":"BMC Bioinformatics"},{"key":"912_CR60","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/1471-2105-6-73","volume":"6","author":"I Holmes","year":"2005","unstructured":"Holmes I: Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 2005, 6: 73. 10.1186\/1471-2105-6-73","journal-title":"BMC Bioinformatics"},{"key":"912_CR61","doi-asserted-by":"publisher","first-page":"2222","DOI":"10.1093\/bioinformatics\/bth229","volume":"20","author":"IL Hofacker","year":"2004","unstructured":"Hofacker IL, Bernhart SH, Stadler PF: Alignment of RNA base pairing probability matrices. Bioinformatics 2004, 20: 2222\u20132227. 10.1093\/bioinformatics\/bth229","journal-title":"Bioinformatics"},{"key":"912_CR62","doi-asserted-by":"publisher","first-page":"1815","DOI":"10.1093\/bioinformatics\/bti279","volume":"21","author":"JK Havgaard","year":"2005","unstructured":"Havgaard JK, Lyngso R, Stormo GD, Gorodkin J: Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 2005, 21: 1815\u20131824. 10.1093\/bioinformatics\/bti279","journal-title":"Bioinformatics"},{"key":"912_CR63","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1126\/science.2468181","volume":"244","author":"M Zuker","year":"1989","unstructured":"Zuker M: On finding all suboptimal foldings of an RNA molecule. Science 1989, 244: 48\u201352.","journal-title":"Science"},{"key":"912_CR64","unstructured":"Mathews lab homepage[http:\/\/rna.urmc.rochester.edu]"},{"key":"912_CR65","first-page":"526","volume":"2","author":"SF Altschul","year":"1985","unstructured":"Altschul SF, Erickson BW: Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage. Mol Biol Evol 1985, 2: 526\u2013538.","journal-title":"Mol Biol Evol"},{"key":"912_CR66","doi-asserted-by":"publisher","first-page":"2433","DOI":"10.1093\/nar\/gki541","volume":"33","author":"PP Gardner","year":"2005","unstructured":"Gardner PP, Wilm A, Washietl S: A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 2005, 33: 2433\u20132439. 10.1093\/nar\/gki541","journal-title":"Nucleic Acids Res"},{"key":"912_CR67","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1145\/130385.130401","volume-title":"Proceedings of the 5th Annual Workshop on Computational Learning Theory","author":"BE Boser","year":"1992","unstructured":"Boser BE, Guyon IM, Vapnik VN: A training algorithm for optimal margin classifiers. In Proceedings of the 5th Annual Workshop on Computational Learning Theory. ACM Press; 1992:144\u2013152."},{"key":"912_CR68","first-page":"273","volume":"20","author":"C Cortes","year":"1995","unstructured":"Cortes C, Vapnik V: Support-vector network. Machine Learning 1995, 20: 273\u2013297.","journal-title":"Machine Learning"},{"key":"912_CR69","unstructured":"Chang CC, Lin CJ: LIBSVM: a library for support vector machines.[http:\/\/www.csie.ntu.edu.tw\/~cjlin\/libsvm]"},{"key":"912_CR70","unstructured":"Gish W: WU BLAST 2.0.[http:\/\/blast.wustl.edu]"},{"key":"912_CR71","doi-asserted-by":"publisher","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","volume":"5","author":"S Kurtz","year":"2004","unstructured":"Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes. Genome Biol 2004, 5: R12. 10.1186\/gb-2004-5-2-r12","journal-title":"Genome Biol"},{"key":"912_CR72","doi-asserted-by":"publisher","first-page":"2294","DOI":"10.1093\/bioinformatics\/bti177","volume":"21","author":"I Holmes","year":"2005","unstructured":"Holmes I: Using evolutionary Expectation Maximization to estimate indel rates. Bioinformatics 2005, 21: 2294\u20132300. 10.1093\/bioinformatics\/bti177","journal-title":"Bioinformatics"},{"key":"912_CR73","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1101\/gr.809403","volume":"13","author":"S Schwartz","year":"2003","unstructured":"Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res 2003, 13: 103\u2013107. 10.1101\/gr.809403","journal-title":"Genome Res"},{"key":"912_CR74","doi-asserted-by":"publisher","first-page":"3724","DOI":"10.1093\/nar\/25.18.3724","volume":"25","author":"J Gorodkin","year":"1997","unstructured":"Gorodkin J, Heyer LJ, Stormo GD: Finding the most significant common sequence and structure in a set of RNA sequences. Nucleic Acids Res 1997, 25: 3724\u20133732. 10.1093\/nar\/25.18.3724","journal-title":"Nucleic Acids Res"},{"key":"912_CR75","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16: 276\u2013277. 10.1016\/S0168-9525(00)02024-2","journal-title":"Trends Genet"},{"key":"912_CR76","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/nar\/28.1.166","volume":"28","author":"M Szymanski","year":"2000","unstructured":"Szymanski M, Barciszewska MZ, Barciszewski J, Erdmann VA: 5S ribosomal RNA database Y2K. Nucleic Acids Res 2000, 28: 166\u2013167. 10.1093\/nar\/28.1.166","journal-title":"Nucleic Acids Res"},{"key":"912_CR77","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1093\/nar\/26.1.148","volume":"26","author":"M Sprinzl","year":"1998","unstructured":"Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S: Compilation of tRNA sequences and sequences of tRNA genes. Nucl Acids Res 1998, 26: 148\u2013153. 10.1093\/nar\/26.1.148","journal-title":"Nucl Acids Res"},{"key":"912_CR78","unstructured":"Clote P: Clote computational biology lab.[http:\/\/clavius.bc.edu\/~clotelab\/]"},{"key":"912_CR79","unstructured":"NCBI Entrez Genome Project database: NCBI Entrez Genome Project database.[http:\/\/www.ncbi.nlm.nih.gov\/genomes\/rnatab.cgi?gi=115&db=Genome]"},{"key":"912_CR80","unstructured":"The Wellcome Trust Sanger Institute S. typhi database: The Wellcome Trust Sanger Institute S. typhi database.[http:\/\/www.sanger.ac.uk\/Projects\/S_typhi\/]"},{"key":"912_CR81","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/1471-2105-3-2","volume":"3","author":"JJ Cannone","year":"2002","unstructured":"Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR: The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002, 3: 2. 10.1186\/1471-2105-3-2","journal-title":"BMC Bioinformatics"},{"key":"912_CR82","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/0378-1119(89)90026-7","volume":"82","author":"F Michel","year":"1989","unstructured":"Michel F, Umesono K, Ozeki H: Comparative and functional anatomy of group II catalytic introns - a review. Gene 1989, 82: 5\u201330. 10.1016\/0378-1119(89)90026-7","journal-title":"Gene"},{"key":"912_CR83","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1093\/nar\/27.1.314","volume":"27","author":"JW Brown","year":"1999","unstructured":"Brown JW: The ribonuclease P database. Nucleic Acids Res 1999, 27: 314. 10.1093\/nar\/27.1.314","journal-title":"Nucleic Acids Res"},{"key":"912_CR84","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1093\/nar\/26.1.177","volume":"26","author":"N Larsen","year":"1998","unstructured":"Larsen N, Samuelsson T, Zwieb C: The signal recognition particle database (SRPDB). Nucleic Acids Res 1998, 26: 177\u2013178. 10.1093\/nar\/26.1.177","journal-title":"Nucleic Acids Res"},{"key":"912_CR85","first-page":"1","volume":"3","author":"DH Mathews","year":"1997","unstructured":"Mathews DH, Banerjee AR, Luan DD, Eickbush TH, Turner DH: Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA 1997, 3: 1\u201316.","journal-title":"RNA"},{"key":"912_CR86","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1261\/rna.5216204","volume":"10","author":"AM Ruschak","year":"2004","unstructured":"Ruschak AM, Mathews DH, Bibillo A, Spinelli SL, Childs JL, Eickbush TH, Turner DH: Secondary structure models of the 3' untranslated regions of diverse R2 RNAs. RNA 2004, 10: 978\u2013987. 10.1261\/rna.5216204","journal-title":"RNA"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-173.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T23:18:11Z","timestamp":1630451891000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-173"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,3,27]]},"references-count":86,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["912"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-173","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.1047833.497848","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,3,27]]},"assertion":[{"value":"30 November 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"173"}}