{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T10:55:48Z","timestamp":1776336948475,"version":"3.51.2"},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using tiling arrays in organisms such as human and <jats:italic>Arabidopsis<\/jats:italic> have revealed a great number of transcripts, a large portion of which have little or no capability to encode proteins. This unexpected finding suggests that the currently known repertoire of ncRNAs may only represent a small fraction of ncRNAs of the organisms. Thus, efficient and effective prediction of ncRNAs has become an important task in bioinformatics in recent years. Among the available computational methods, the comparative genomic approach seems to be the most powerful to detect ncRNAs. The recent completion of the sequencing of several major plant genomes has made the approach possible for plants.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed a pipeline to predict novel ncRNAs in the <jats:italic>Arabidopsis<\/jats:italic> (<jats:italic>Arabidopsis thaliana<\/jats:italic>) genome. It starts by comparing the expressed intergenic regions of <jats:italic>Arabidopsis<\/jats:italic> as provided in two whole-genome high-density oligo-probe arrays from the literature with the intergenic nucleotide sequences of all completely sequenced plant genomes including rice (<jats:italic>Oryza sativa<\/jats:italic>), poplar (<jats:italic>Populus trichocarpa<\/jats:italic>), grape (<jats:italic>Vitis vinifera<\/jats:italic>), and papaya (<jats:italic>Carica papaya<\/jats:italic>). By using multiple sequence alignment, a popular ncRNA prediction program (RNAz), wet-bench experimental validation, protein-coding potential analysis, and stringent screening against various ncRNA databases, the pipeline resulted in 16 families of novel ncRNAs (with a total of 21 ncRNAs).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>In this paper, we undertake a genome-wide search for novel ncRNAs in the genome of <jats:italic>Arabidopsis<\/jats:italic> by a comparative genomics approach. The identified novel ncRNAs are evolutionarily conserved between <jats:italic>Arabidopsis<\/jats:italic> and other recently sequenced plants, and may conduct interesting novel biological functions.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-s1-s36","type":"journal-article","created":{"date-parts":[[2009,1,30]],"date-time":"2009-01-30T20:05:03Z","timestamp":1233345903000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["Computational prediction of novel non-coding RNAs in Arabidopsis thaliana"],"prefix":"10.1186","volume":"10","author":[{"given":"Dandan","family":"Song","sequence":"first","affiliation":[]},{"given":"Yang","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Bin","family":"Yu","sequence":"additional","affiliation":[]},{"given":"Binglian","family":"Zheng","sequence":"additional","affiliation":[]},{"given":"Zhidong","family":"Deng","sequence":"additional","affiliation":[]},{"given":"Bao-Liang","family":"Lu","sequence":"additional","affiliation":[]},{"given":"Xuemei","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Tao","family":"Jiang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,1,30]]},"reference":[{"key":"3219_CR1","volume-title":"Role of Histone H3 Lysine 27 Methylation in X Inactivation","author":"K Plath","year":"2003","unstructured":"Plath K, Fang J, Mlynarczyk-Evans S, Cao R, Worringer K, Wang H, de la Cruz C, Otte A, Panning B, Zhang Y: Role of Histone H3 Lysine 27 Methylation in X Inactivation. 2003."},{"issue":"7","key":"3219_CR2","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1016\/j.cell.2007.05.022","volume":"129","author":"J Rinn","year":"2007","unstructured":"Rinn J, Kertesz M, Wang J, Squazzo S, Xu X, Brugmann S, Goodnough L, Helms J, Farnham P, Segal E, et al.: Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs. Cell 2007, 129(7):1311\u20131323. 10.1016\/j.cell.2007.05.022","journal-title":"Cell"},{"issue":"5646","key":"3219_CR3","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1126\/science.1088305","volume":"302","author":"K Yamada","year":"2003","unstructured":"Yamada K, Lim J, Dale J, Chen H, Shinn P, Palm C, Southwick A, Wu H, Kim C, Nguyen M, et al.: Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome. Science 2003, 302(5646):842\u2013846. 10.1126\/science.1088305","journal-title":"Science"},{"issue":"12","key":"3219_CR4","doi-asserted-by":"publisher","first-page":"4453","DOI":"10.1073\/pnas.0408203102","volume":"102","author":"V Stolc","year":"2005","unstructured":"Stolc V, Samanta M, Tongprasit W, Sethi H, Liang S, Nelson D, Hegeman A, Nelson C, Rancour D, Bednarek S, et al.: Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proceedings of the National Academy of Sciences 2005, 102(12):4453. 10.1073\/pnas.0408203102","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"Suppl 1","key":"3219_CR5","doi-asserted-by":"publisher","first-page":"S14","DOI":"10.1186\/1471-2148-7-S1-S14","volume":"7","author":"Z Zhang","year":"2007","unstructured":"Zhang Z, Pang A, Gerstein M: Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. BMC Evolutionary Biology 2007, 7(Suppl 1):S14. 10.1186\/1471-2148-7-S1-S14","journal-title":"BMC Evolutionary Biology"},{"issue":"3","key":"3219_CR6","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1104\/pp.010501","volume":"127","author":"G MacIntosh","year":"2001","unstructured":"MacIntosh G, Wilkerson C, Green P: Identification and Analysis of Arabidopsis Expressed Sequence Tags Characteristic of Non-Coding RNAs. Plant Physiology 2001, 127(3):765. 10.1104\/pp.010501","journal-title":"Plant Physiology"},{"key":"3219_CR7","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1038\/nbt1144","volume":"23","author":"S Washietl","year":"2005","unstructured":"Washietl S, Hofacker I, Lukasser M, H\u00c4uttenhofer A, Stadler P: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nature Biotechnology 2005, 23: 1383\u20131390. 10.1038\/nbt1144","journal-title":"Nature Biotechnology"},{"issue":"Database issue","key":"3219_CR8","doi-asserted-by":"publisher","first-page":"121","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(Database issue):121\u2013124. 10.1093\/nar\/gki081","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"3219_CR9","doi-asserted-by":"publisher","first-page":"D140","DOI":"10.1093\/nar\/gkj112","volume":"34","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 issue):D140-D144. 10.1093\/nar\/gkj112","journal-title":"Nucleic Acids Res"},{"key":"3219_CR10","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1093\/nar\/gkg009","volume":"31","author":"J Brown","year":"2003","unstructured":"Brown J, Echeverria M, Qu L, Lowe T, Bachellerie J, H\u00c4uttenhofer A, Kastenmayer J, Green P, Shaw P, Marshall D: Plant snoRNA database. Nucleic Acids Res 2003, 31: 432\u2013435. 10.1093\/nar\/gkg009","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"3219_CR11","doi-asserted-by":"publisher","first-page":"2079","DOI":"10.1093\/nar\/22.11.2079","volume":"22","author":"S Eddy","year":"1994","unstructured":"Eddy S, Durbin R: RNA sequence analysis using covariance models. Nucleic Acids Res 1994, 22(11):2079\u20132088. 10.1093\/nar\/22.11.2079","journal-title":"Nucleic Acids Res"},{"key":"3219_CR12","first-page":"1983","volume-title":"Proc IEEE Workshop on Statistical Signal Processing, Bordeaux, France","author":"B Yoon","year":"2005","unstructured":"Yoon B, Vaidyanthan P: An overview of the role of context-sensitive HMMs in the prediction of ncRNA genes. Proc IEEE Workshop on Statistical Signal Processing, Bordeaux, France 2005, 1983\u20131984."},{"issue":"4","key":"3219_CR13","doi-asserted-by":"publisher","first-page":"e65","DOI":"10.1371\/journal.pcbi.0030065","volume":"3","author":"S Will","year":"2007","unstructured":"Will S, Reiche K, Hofacker I, Stadler P, Backofen R: Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol 2007, 3(4):e65. 10.1371\/journal.pcbi.0030065","journal-title":"PLoS Comput Biol"},{"key":"3219_CR14","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1101\/gr.2908205","volume":"15","author":"A Adai","year":"2005","unstructured":"Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V: Computational prediction of miRNAs in Arabidopsis thaliana. Genome Research 2005, 15: 78. 10.1101\/gr.2908205","journal-title":"Genome Research"},{"issue":"2","key":"3219_CR15","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1101\/gr.6887408","volume":"18","author":"E Torarinsson","year":"2008","unstructured":"Torarinsson E, Yao Z, Wiklund E, Bramsen J, Hansen C, Kjems J, Tommerup N, Ruzzo W, Gorodkin J: Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Research 2008, 18(2):242. 10.1101\/gr.6887408","journal-title":"Genome Research"},{"issue":"14","key":"3219_CR16","doi-asserted-by":"publisher","first-page":"4119","DOI":"10.1093\/nar\/gkg438","volume":"31","author":"J McCutcheon","year":"2003","unstructured":"McCutcheon J, Eddy S: Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Research 2003, 31(14):4119. 10.1093\/nar\/gkg438","journal-title":"Nucleic Acids Research"},{"key":"3219_CR17","volume-title":"BMC Bioinformatics","author":"E Rivas","year":"2001","unstructured":"Rivas E, Eddy S: Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001., 2(8):","edition":"2"},{"issue":"9","key":"3219_CR18","doi-asserted-by":"publisher","first-page":"R73","DOI":"10.1186\/gb-2005-6-9-r73","volume":"6","author":"I Axmann","year":"2005","unstructured":"Axmann I, Kensche P, Vogel J, Kohl S, Herzel H, Hess W: Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol 2005, 6(9):R73. 10.1186\/gb-2005-6-9-r73","journal-title":"Genome Biol"},{"issue":"14","key":"3219_CR19","doi-asserted-by":"publisher","first-page":"4809","DOI":"10.1093\/nar\/gkm487","volume":"35","author":"Z Weinberg","year":"2007","unstructured":"Weinberg Z, Barrick J, Yao Z, Roth A, Kim J, Gore J, Wang J, Lee E, Block K, Sudarsan N, et al.: Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research 2007, 35(14):4809. 10.1093\/nar\/gkm487","journal-title":"Nucleic Acids Research"},{"issue":"7","key":"3219_CR20","doi-asserted-by":"publisher","first-page":"1340","DOI":"10.1016\/j.cell.2007.10.056","volume":"131","author":"J Chekanova","year":"2007","unstructured":"Chekanova J, Gregory B, Reverdatto S, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, et al.: Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome. Cell 2007, 131(7):1340\u20131353. 10.1016\/j.cell.2007.10.056","journal-title":"Cell"},{"key":"3219_CR21","unstructured":"TAIR[http:\/\/www.arabidopsis.org]"},{"key":"3219_CR22","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1093\/nar\/gkm952","volume":"36","author":"S Griffiths-Jones","year":"2008","unstructured":"Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Research 2008, 36: 154\u2013158. 10.1093\/nar\/gkm952","journal-title":"Nucleic Acids Research"},{"key":"3219_CR23","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1093\/nar\/gkh023","volume":"32","author":"S Griffiths-Jones","year":"2004","unstructured":"Griffiths-Jones S: The microRNA Registry. Nucleic Acids Research 2004, 32: 109\u2013111. 10.1093\/nar\/gkh023","journal-title":"Nucleic Acids Research"},{"key":"3219_CR24","unstructured":"EMBL[http:\/\/www.ebi.ac.uk\/GenomeReviews\/files\/cellular\/]"},{"issue":"7","key":"3219_CR25","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.tplants.2008.02.009","volume":"13","author":"L Rymarquis","year":"2008","unstructured":"Rymarquis L, Kastenmayer J, H\u00fcttenhofer A, Green P: Diamonds in the rough: mRNA-like non-coding RNAs. Trends in Plant Science 2008, 13(7):329\u2013334. 10.1016\/j.tplants.2008.02.009","journal-title":"Trends in Plant Science"},{"key":"3219_CR26","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/1471-2105-3-18","volume":"3","author":"SR Eddy","year":"2002","unstructured":"Eddy SR: A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 2002, 3: 18. 10.1186\/1471-2105-3-18","journal-title":"BMC Bioinformatics"},{"key":"3219_CR27","unstructured":"Tatusov T, Tatusov R: ORF Finder (Open Reading Frame Finder). Software [http:\/\/www.ncbi.nlm.nih.gov\/projects\/gorf\/]"},{"key":"3219_CR28","volume-title":"Biometry: The Principles and Practice of Statistics in Biological Research (ed.)","author":"R Sokal","year":"1995","unstructured":"Sokal R, Rohlf F: Biometry: The Principles and Practice of Statistics in Biological Research (ed.). 1995."},{"key":"3219_CR29","unstructured":"ASRP database[http:\/\/asrp.cgrb.oregonstate.edu\/]"},{"issue":"5565","key":"3219_CR30","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1126\/science.1068037","volume":"296","author":"JY","year":"2002","unstructured":"JY , et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296(5565):79\u201392. 10.1126\/science.1068037","journal-title":"Science"},{"key":"3219_CR31","unstructured":"Rice Genome Annotation Project[http:\/\/rice.plantbiology.msu.edu]"},{"issue":"5793","key":"3219_CR32","doi-asserted-by":"publisher","first-page":"1596","DOI":"10.1126\/science.1128691","volume":"313","author":"G Tuskan","year":"2006","unstructured":"Tuskan G, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, et al.: The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313(5793):1596\u20131604. 10.1126\/science.1128691","journal-title":"Science"},{"issue":"7161","key":"3219_CR33","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1038\/nature06148","volume":"449","author":"O Jaillon","year":"2007","unstructured":"Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al.: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007, 449(7161):463\u2013467. 10.1038\/nature06148","journal-title":"Nature"},{"issue":"7190","key":"3219_CR34","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1038\/nature06856","volume":"452","author":"R Ming","year":"2008","unstructured":"Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw J, Senin P, Wang W, Ly B, Lewis K, et al.: The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 2008, 452(7190):991\u2013996. 10.1038\/nature06856","journal-title":"Nature"},{"issue":"22","key":"3219_CR35","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"J Thompson","year":"1994","unstructured":"Thompson J, Higgins D, Gibson T, et al.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673\u20134680. 10.1093\/nar\/22.22.4673","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"3219_CR36","doi-asserted-by":"publisher","first-page":"2454","DOI":"10.1073\/pnas.0409169102","volume":"102","author":"S Washietl","year":"2005","unstructured":"Washietl S, Hofacker I, Stadler P: From The Cover: Fast and reliable prediction of noncoding RNAs. Proceedings of the National Academy of Sciences 2005, 102(7):2454. 10.1073\/pnas.0409169102","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"3219_CR37","first-page":"78","volume-title":"ECCB\/JBI (Supplement of Bioinformatics)","author":"K Missal","year":"2005","unstructured":"Missal K, Rose D, Stadler PF: Non-coding RNAs in Ciona intestinalis. ECCB\/JBI (Supplement of Bioinformatics) 2005, 78."},{"key":"3219_CR38","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1101\/gr.6836108","volume":"18","author":"T Mourier","year":"2008","unstructured":"Mourier T, Carret C, Kyes K, Christodoulou Z, Gardner P, Jeffares D, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, Ivens A, Newbold C, Pain A: Genome wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Genome Research 2008, 18: 281\u2013292. 10.1101\/gr.6836108","journal-title":"Genome Research"},{"key":"3219_CR39","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"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S1-S36.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T10:49:18Z","timestamp":1630493358000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S1-S36"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1]]},"references-count":39,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2009,1]]}},"alternative-id":["3219"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s1-s36","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,1]]},"assertion":[{"value":"30 January 2009","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S36"}}