{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:53:40Z","timestamp":1732035220196},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"S9","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,9]]},"DOI":"10.1186\/1471-2105-15-s9-s15","type":"journal-article","created":{"date-parts":[[2014,9,10]],"date-time":"2014-09-10T15:04:14Z","timestamp":1410361454000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search"],"prefix":"10.1186","volume":"15","author":[{"given":"Ping","family":"Ge","sequence":"first","affiliation":[]},{"given":"Cuncong","family":"Zhong","sequence":"additional","affiliation":[]},{"given":"Shaojie","family":"Zhang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,9,10]]},"reference":[{"key":"6576_CR1","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. Nature Review Genetics. 2001, 2: 919-929. 10.1038\/35103511.","journal-title":"Nature Review Genetics"},{"key":"6576_CR2","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1126\/science.1072249","volume":"296","author":"G Storz","year":"2002","unstructured":"Storz G: An expanding universe of noncoding RNAs. Science. 2002, 296: 1260-1263. 10.1126\/science.1072249.","journal-title":"Science"},{"issue":"3","key":"6576_CR3","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1038\/nrg2521","volume":"10","author":"TR Mercer","year":"2009","unstructured":"Mercer TR, Dinger ME, Mattick JS: Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009, 10 (3): 155-159. 10.1038\/nrg2521.","journal-title":"Nat Rev Genet"},{"key":"6576_CR4","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/j.sbi.2005.05.003","volume":"15","author":"BJ Tucker","year":"2005","unstructured":"Tucker BJ, Breaker RR: Riboswitches as versatile gene control elements. Curr Opin Struct Biol. 2005, 15: 342-348. 10.1016\/j.sbi.2005.05.003.","journal-title":"Curr Opin Struct Biol"},{"key":"6576_CR5","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1146\/annurev.biophys.30.1.457","volume":"30","author":"EA Doherty","year":"2001","unstructured":"Doherty EA, Doudna JA: Ribozyme structures and mechanisms. Annu Rev Biophys Biomol Struct. 2001, 30: 457-475. 10.1146\/annurev.biophys.30.1.457.","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"7","key":"6576_CR6","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1261\/rna.2080205","volume":"11","author":"T Hainzl","year":"2005","unstructured":"Hainzl T, Huang S, Sauer-Eriksson AE: Structural insights into SRP RNA: an induced fit mechanism for SRP assembly. RNA. 2005, 11 (7): 1043-1050. 10.1261\/rna.2080205.","journal-title":"RNA"},{"issue":"7","key":"6576_CR7","doi-asserted-by":"publisher","first-page":"1576","DOI":"10.1093\/nar\/26.7.1576","volume":"26","author":"J Cavaille","year":"1998","unstructured":"Cavaille J, Bachellerie JP: SnoRNA-guided ribose methylation of rRNA: structural features of the guide RNA duplex influencing the extent of the reaction. Nucleic Acids Res. 1998, 26 (7): 1576-1587. 10.1093\/nar\/26.7.1576.","journal-title":"Nucleic Acids Res"},{"issue":"7414","key":"6576_CR8","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"BE Bernstein","year":"2012","unstructured":"Bernstein BE, Birney E, Dunham I, Green ED: An integrated encyclopedia of DNA elements in the human genome. Nature. 2012, 489 (7414): 57-74. 10.1038\/nature11247.","journal-title":"Nature"},{"issue":"7146","key":"6576_CR9","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nature05874","volume":"447","author":"E Birney","year":"2007","unstructured":"Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447 (7146): 799-816. 10.1038\/nature05874.","journal-title":"Nature"},{"issue":"12","key":"6576_CR10","doi-asserted-by":"publisher","first-page":"1975","DOI":"10.1101\/gr.202401","volume":"11","author":"GK Wong","year":"2001","unstructured":"Wong GK, Passey DA, Yu J: Most of the human genome is transcribed. Genome Res. 2001, 11 (12): 1975-1977. 10.1101\/gr.202401.","journal-title":"Genome Res"},{"issue":"13","key":"6576_CR11","doi-asserted-by":"publisher","first-page":"3406","DOI":"10.1093\/nar\/gkg595","volume":"31","author":"M Zuker","year":"2003","unstructured":"Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31 (13): 3406-3415. 10.1093\/nar\/gkg595.","journal-title":"Nucleic Acids Res"},{"key":"6576_CR12","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 LS, Tacker M, Schuster P: Fast folding and comparison of RNA secondary structures. Monatsh Chem. 1994, 125: 167-188. 10.1007\/BF00818163.","journal-title":"Monatsh Chem"},{"key":"6576_CR13","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1186\/1471-2105-11-129","volume":"11","author":"JS Reuter","year":"2010","unstructured":"Reuter JS, Mathews DH: RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 2010, 11: 129-10.1186\/1471-2105-11-129.","journal-title":"BMC Bioinformatics"},{"key":"6576_CR14","doi-asserted-by":"crossref","unstructured":"Hajiaghayi M, Condon A, Hoos HH: Analysis of energy-based algorithms for RNA secondary structure prediction. BMC Bioinformatics. 2012, 13 (22):","DOI":"10.1186\/1471-2105-13-22"},{"key":"6576_CR15","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 USA. 2005, 102: 2454-2459. 10.1073\/pnas.0409169102.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6576_CR16","first-page":"69","volume":"15","author":"AR Gruber","year":"2010","unstructured":"Gruber AR, Findeiss S, Washietl S, Hofacker IL, Stadler PF: RNAZ 2.0: improved noncoding RNA detection. Pac Symp Biocomput. 2010, 15: 69-79.","journal-title":"Pac Symp Biocomput"},{"key":"6576_CR17","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1007\/978-1-59745-514-5_33","volume":"395","author":"IL Hofacker","year":"2007","unstructured":"Hofacker IL: RNA consensus structure prediction with RNAalifold. Methods Mol Biol. 2007, 395: 527-544. 10.1007\/978-1-59745-514-5_33.","journal-title":"Methods Mol Biol"},{"issue":"4","key":"6576_CR18","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1371\/journal.pcbi.0020033","volume":"2","author":"JS Pedersen","year":"2006","unstructured":"Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D: Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006, 2 (4): 33-10.1371\/journal.pcbi.0020033.","journal-title":"PLoS Comput Biol"},{"key":"6576_CR19","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/1471-2105-14-142","volume":"14","author":"P Ge","year":"2013","unstructured":"Ge P, Zhang S: Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction. BMC Bioinformatics. 2013, 14: 142-10.1186\/1471-2105-14-142.","journal-title":"BMC Bioinformatics"},{"issue":"22","key":"6576_CR20","doi-asserted-by":"publisher","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","volume":"29","author":"EP Nawrocki","year":"2013","unstructured":"Nawrocki EP, Eddy SR: Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013, 29 (22): 2933-2935. 10.1093\/bioinformatics\/btt509.","journal-title":"Bioinformatics"},{"issue":"Database","key":"6576_CR21","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1093\/nar\/gks1005","volume":"41","author":"SW Burge","year":"2013","unstructured":"Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A: Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2013, 41 (Database): 226-232.","journal-title":"Nucleic Acids Res"},{"key":"6576_CR22","first-page":"583","volume-title":"Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs","author":"E Rivas","year":"2000","unstructured":"Rivas E, Eddy SR: Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. 2000, 16 (7): 583-605."},{"key":"6576_CR23","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1038\/nature09322","volume":"467","author":"M Kertesz","year":"2010","unstructured":"Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E: Genome-wide measurement of RNA secondary structure in yeast. Nature. 2010, 467: 103-107. 10.1038\/nature09322.","journal-title":"Nature"},{"key":"6576_CR24","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1038\/nmeth.1529","volume":"7","author":"JG Underwood","year":"2010","unstructured":"Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D: FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010, 7: 995-1001. 10.1038\/nmeth.1529.","journal-title":"Nat Methods"},{"key":"6576_CR25","doi-asserted-by":"publisher","first-page":"11063","DOI":"10.1073\/pnas.1106501108","volume":"108","author":"JB Lucks","year":"2011","unstructured":"Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP: Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci USA. 2011, 108: 11063-11068. 10.1073\/pnas.1106501108.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"6576_CR26","doi-asserted-by":"publisher","first-page":"1001141","DOI":"10.1371\/journal.pgen.1001141","volume":"6","author":"Q Zheng","year":"2010","unstructured":"Zheng Q, Ryvkin P, Li F, Dragomir I, Valladares O, Yang J, Cao K, Wang LS, Gregory BD: Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet. 2010, 6 (9): 1001141-10.1371\/journal.pgen.1001141.","journal-title":"PLoS Genet"},{"issue":"1","key":"6576_CR27","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.celrep.2011.10.002","volume":"1","author":"F Li","year":"2012","unstructured":"Li F, Zheng Q, Ryvkin P, Dragomir I, Desai Y, Aiyer S, Valladares O, Yang J, Bambina S, Sabin LR, Murray JI, Lamitina T, Raj A, Cherry S, Wang LS, Gregory BD: Global analysis of RNA secondary structure in two metazoans. Cell Rep. 2012, 1 (1): 69-82. 10.1016\/j.celrep.2011.10.002.","journal-title":"Cell Rep"},{"key":"6576_CR28","volume-title":"Nature","author":"Y Ding","year":"2013","unstructured":"Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM: In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature. 2013"},{"issue":"3","key":"6576_CR29","doi-asserted-by":"publisher","first-page":"1610","DOI":"10.1038\/nprot.2006.249","volume":"1","author":"KA Wilkinson","year":"2006","unstructured":"Wilkinson KA, Merino EJ, Weeks KM: Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc. 2006, 1 (3): 1610-1616. 10.1038\/nprot.2006.249.","journal-title":"Nat Protoc"},{"issue":"1","key":"6576_CR30","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1073\/pnas.0806929106","volume":"106","author":"KE Deigan","year":"2009","unstructured":"Deigan KE, Li TW, Mathews DH, Weeks KM: Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci USA. 2009, 106 (1): 97-102. 10.1073\/pnas.0806929106.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"10","key":"6576_CR31","doi-asserted-by":"publisher","first-page":"45160","DOI":"10.1371\/journal.pone.0045160","volume":"7","author":"K Zarringhalam","year":"2012","unstructured":"Zarringhalam K, Meyer MM, Dotu I, Chuang JH, Clote P: Integrating chemical footprinting data into RNA secondary structure prediction. PLoS ONE. 2012, 7 (10): 45160-10.1371\/journal.pone.0045160.","journal-title":"PLoS ONE"},{"issue":"2","key":"6576_CR32","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1142\/S0219720009004126","volume":"7","author":"HH Tseng","year":"2009","unstructured":"Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL: Finding non-coding RNAs through genome-scale clustering. J Bioinform Comput Biol. 2009, 7 (2): 373-388. 10.1142\/S0219720009004126.","journal-title":"J Bioinform Comput Biol"},{"issue":"5","key":"6576_CR33","doi-asserted-by":"publisher","first-page":"1602","DOI":"10.1093\/nar\/gkn1084","volume":"37","author":"J Hertel","year":"2009","unstructured":"Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF: Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res. 2009, 37 (5): 1602-1615. 10.1093\/nar\/gkn1084.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"6576_CR34","doi-asserted-by":"publisher","first-page":"2807","DOI":"10.1093\/nar\/gks1283","volume":"41","author":"Z Sukosd","year":"2013","unstructured":"Sukosd Z, Swenson MS, Kjems J, Heitsch CE: Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. Nucleic Acids Res. 2013, 41 (5): 2807-2816. 10.1093\/nar\/gks1283.","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"6576_CR35","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1093\/bioinformatics\/btl113","volume":"22","author":"Y Ponty","year":"2006","unstructured":"Ponty Y, Termier M, Denise A: Genrgens: Software for generating random genomic sequences and structures. Bioinformatics. 2006, 22 (12): 1534-1535. 10.1093\/bioinformatics\/btl113.","journal-title":"Bioinformatics"},{"key":"6576_CR36","volume-title":"Cambridge University Press, Cambridge, UK","author":"R Durbin","year":"1998","unstructured":"Durbin R, Eddy SR, Krogh A, Mitchison G: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK. 1998"},{"key":"6576_CR37","volume-title":"PhD thesis","author":"E Nawrocki","year":"2009","unstructured":"Nawrocki E: Structural RNA homology search and alignment using covariance models. PhD thesis. 2009"},{"issue":"1-4","key":"6576_CR38","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1159\/000084979","volume":"110","author":"J Jurka","year":"2005","unstructured":"Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005, 110 (1-4): 462-467. 10.1159\/000084979.","journal-title":"Cytogenet Genome Res"},{"issue":"13","key":"6576_CR39","doi-asserted-by":"publisher","first-page":"1679","DOI":"10.1101\/gad.1449106","volume":"20","author":"JM Izquierdo","year":"2006","unstructured":"Izquierdo JM, Valcarcel J: A simple principle to explain the evolution of pre-mRNA splicing. Genes Dev. 2006, 20 (13): 1679-1684. 10.1101\/gad.1449106.","journal-title":"Genes Dev"},{"issue":"12","key":"6576_CR40","doi-asserted-by":"publisher","first-page":"6300","DOI":"10.1093\/nar\/gkt316","volume":"41","author":"I Livyatan","year":"2013","unstructured":"Livyatan I, Harikumar A, Nissim-Rafinia M, Duttagupta R, Gingeras TR, Meshorer E: Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation. Nucleic Acids Res. 2013, 41 (12): 6300-6315. 10.1093\/nar\/gkt316.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"6576_CR41","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1093\/hmg\/ddp585","volume":"19","author":"S Kishore","year":"2010","unstructured":"Kishore S, Khanna A, Zhang Z, Hui J, Balwierz PJ, Stefan M, Beach C, Nicholls RD, Zavolan M, Stamm S: The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum Mol Genet. 2010, 19 (7): 1153-1164. 10.1093\/hmg\/ddp585.","journal-title":"Hum Mol Genet"},{"key":"6576_CR42","first-page":"52","volume-title":"Proc IEEE Comput Syst Bioinform Conf","author":"V Bafna","year":"2004","unstructured":"Bafna V, Zhang S: FastR: fast database search tool for non-coding RNA. Proc IEEE Comput Syst Bioinform Conf. 2004, 52-61."},{"issue":"14","key":"6576_CR43","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1093\/bioinformatics\/btl232","volume":"22","author":"S Zhang","year":"2006","unstructured":"Zhang S, Borovok I, Aharonowitz Y, Sharan R, Bafna V: A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. Bioinformatics. 2006, 22 (14): 557-565. 10.1093\/bioinformatics\/btl232.","journal-title":"Bioinformatics"},{"key":"6576_CR44","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/1471-2105-4-44","volume":"4","author":"SR Eddy","year":"2003","unstructured":"Eddy SR, Klein RJ: RSEARCH:finding homologs of single structured RNA sequences. BMC Bioinformatics. 2003, 4: 44-10.1186\/1471-2105-4-44.","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S9-S15.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T18:49:45Z","timestamp":1630608585000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S9-S15"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9]]},"references-count":44,"journal-issue":{"issue":"S9","published-print":{"date-parts":[[2014,9]]}},"alternative-id":["6576"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s9-s15","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,9]]},"assertion":[{"value":"10 September 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S15"}}