Detecting and comparing non-coding RNAs in the high-throughput era

International Journal of Molecular Sciences

Volumn 14, Issue 8, 2013, Pages 15423-15458

  Bussotti, Giovanni ^a   Notredame, Cedric ^b   Enright, Anton J ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

Comparative biology; High throughput; LncRNAs; ncRNAs; RNA seq; Sequencing

Indexed keywords

LONG UNTRANSLATED RNA; UNTRANSLATED RNA;

ACCURACY; BIOINFORMATICS; CELL FUNCTION; CRYSTALLIZATION; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; HIGH THROUGHPUT SEQUENCING; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; REVIEW; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; THERMODYNAMICS;

BASE SEQUENCE; GENOMICS; HIGH-THROUGHPUT SCREENING ASSAYS; NUCLEIC ACID CONFORMATION; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA, UNTRANSLATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 84880720364     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms140815423     Document Type: Review

References (262)

1. Lee, R.C.; Feinbaum, R.L.; Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75, 843-854.
2. Brown, C.J.; Hendrich, B.D.; Rupert, J.L.; Lafreniere, R.G.; Xing, Y.; Lawrence, J.; Willard, H.F. The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992, 71, 527-542.
3. Farazi, T.A.; Juranek, S.A.; Tuschl, T. The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 2008, 135, 1201-1214.
4. Bachellerie, J.P.; Cavaille, J.; Huttenhofer, A. The expanding snoRNA world. Biochimie 2002, 84, 775-790.
5. Barrett, T.; Suzek, T.O.; Troup, D.B.; Wilhite, S.E.; Ngau, W.C.; Ledoux, P.; Rudnev, D.; Lash, A.E.; Fujibuchi, W.; Edgar, R. NCBI GEO: Mining millions of expression profiles- database and tools. Nucleic Acids Res. 2005, 33, D562-D566.
6. Parkinson, H.; Sarkans, U.; Shojatalab, M.; Abeygunawardena, N.; Contrino, S.; Coulson, R.; Farne, A.; Lara, G.G.; Holloway, E. et al. ArrayExpress-A public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2005, 33, D553-D555.
7. Griffiths-Jones, S.; Grocock, R.J.; van Dongen, S.; Bateman, A.; Enright, A.J. miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006, 34, D140-D144.
8. Fraser, B.A.; Weadick, C.J.; Janowitz, I.; Rodd, F.H.; Hughes, K.A. Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. BMC Genomics 2011, 12, 202.
9. Tuda, J.; Mongan, A.E.; Tolba, M.E.; Imada, M.; Yamagishi, J.; Xuan, X.; Wakaguri, H.; Sugano, S.; Sugimoto, C.; Suzuki, Y. Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2010 update. Nucleic Acids Res. 2011, 39, D625-D631.
10. Mamidala, P.; Wijeratne, A.J.; Wijeratne, S.; Kornacker, K.; Sudhamalla, B.; Rivera-Vega, L.J.; Hoelmer, A.; Meulia, T.; Jones, S.C.; Mittapalli, O. RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug. BMC Genomics 2012, 13, 6.
11. Dinger, M.E.; Amaral, P.P.; Mercer, T.R.; Pang, K.C.; Bruce, S.J.; Gardiner, B.B.; Askarian-Amiri, M.E.; Ru, K.; Solda, G.; Simons, C. et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008, 18, 1433-1445.
12. Okazaki, Y.; Furuno, M.; Kasukawa, T.; Adachi, J.; Bono, H.; Kondo, S.; Nikaido, I.; Osato, N.; Saito, R.; Suzuki, H. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420, 563-573.
13. Guttman, M.; Amit, I.; Garber, M.; French, C.; Lin, M.F.; Feldser, D.; Huarte, M.; Zuk, O.; Carey, B.W.; Cassady, J.P. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458, 223-227.
14. Harrow, J.; Frankish, A.; Gonzalez, J.M.; Tapanari, E.; Diekhans, M.; Kokocinski, F.; Aken, B.L.; Barrell, D.; Zadissa, A.; Searle, S. et al. GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res. 2012, 22, 1760-1774.
15. Managadze, D.; Lobkovsky, A.E.; Wolf, Y.I.; Shabalina, S.A.; Rogozin, I.B.; Koonin, E.V. The vast, conserved mammalian lincRNome. PLoS Comput. Biol. 2013, 9, e1002917.
16. Mattick, J.S.; Gagen, M.J. The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol. 2001, 18, 1611-1630.
17. Mattick, J.S. Non-coding RNAs: The architects of eukaryotic complexity. EMBO Rep. 2001, 2, 986-991.
18. Crick, F.H. On protein synthesis. Symp. Soc. Exp. Biol. 1958, 12, 138-163.
19. Wang, J.; Zhang, J.; Zheng, H.; Li, J.; Liu, D.; Li, H.; Samudrala, R.; Yu, J.; Wong, G.K. Mouse transcriptome: Neutral evolution of "non-coding" complementary DNAs. Nature 2004, 431, doi:10.1038/nature03016.
20. Dinger, M.E.; Pang, K.C.; Mercer, T.R.; Crowe, M.L.; Grimmond, S.M.; Mattick, J.S. NRED: A database of long noncoding RNA expression. Nucleic Acids Res. 2009, 37, D122-D126.
21. Mattick, J.S. The genetic signatures of noncoding RNAs. PLoS Genet. 2009, 5, e1000459.
22. Wapinski, O.; Chang, H.Y. Long noncoding RNAs and human disease. Trends Cell. Biol. 2011, 21, 354-361.
23. Wang, X.; Song, X.; Glass, C.K.; Rosenfeld, M.G. The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs. Cold Spring Harb. Perspect. Biol. 2011, 3, a003756.
24. Satterlee, J.S.; Barbee, S.; Jin, P.; Krichevsky, A.; Salama, S.; Schratt, G.; Wu, D.Y. Noncoding RNAs in the brain. J. Neurosci. 2007, 27, 11856-11859.
25. Mercer, T.R.; Dinger, M.E.; Sunkin, S.M.; Mehler, M.F.; Mattick, J.S. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. USA 2008, 105, 716-721.
26. Kaikkonen, M.U.; Lam, M.T.; Glass, C.K. Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc. Res. 2011, 90, 430-440.
27. Braidotti, G.; Baubec, T.; Pauler, F.; Seidl, C.; Smrzka, O.; Stricker, S.; Yotova, I.; Barlow, D.P. The Air noncoding RNA: An imprinted cis-silencing transcript. Cold Spring Harb. Symp. Quant. Biol. 2004, 69, 55-66.
28. Willingham, A.T.; Orth, A.P.; Batalov, S.; Peters, E.C.; Wen, B.G.; Aza-Blanc, P.; Hogenesch, J.B.; Schultz, P.G. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 2005, 309, 1570-1573.
29. Cesana, M.; Cacchiarelli, D.; Legnini, I.; Santini, T.; Sthandier, O.; Chinappi, M.; Tramontano, A.; Bozzoni, I. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 2011, 147, 358-369.
30. Orom, U.A.; Derrien, T.; Beringer, M.; Gumireddy, K.; Gardini, A.; Bussotti, G.; Lai, F.; Zytnicki, M.; Notredame, C.; Huang, Q, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010, 143, 46-58.
31. Lai, F.; Orom, U.A.; Cesaroni, M.; Beringer, M.; Taatjes, D.J.; Blobel, G.A.; Shiekhattar, R. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 2013, 494, 497-501.
32. Rinn, J.L.; Chang, H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 2012, 81, 145-166.
33. Amaral, P.P.; Clark, M.B.; Gascoigne, D.K.; Dinger, M.E.; Mattick, J.S. lncRNAdb: A reference database for long noncoding RNAs. Nucleic Acids Res. 2011, 39, D146-D151.
34. Ravasi, T.; Suzuki, H.; Pang, K.C.; Katayama, S.; Furuno, M.; Okunishi, R.; Fukuda, S.; Ru, K.; Frith, M.C.; Gongora, M.M. et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res. 2006, 16, 11-19.
35. Wang, X.; Arai, S.; Song, X.; Reichart, D.; Du, K.; Pascual, G.; Tempst, P.; Rosenfeld, M.G.; Glass, C.K.; Kurokawa, R. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008, 454, 126-130.
36. Rinn, J.L.; Kertesz, M.; Wang, J.K.; Squazzo, S.L.; Xu, X.; Brugmann, S.A.; Goodnough, L.H.; Helms, J.A.; Farnham, P.J.; Segal, E. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 129, 1311-1323.
37. Rodriguez, A.; Griffiths-Jones, S.; Ashurst, J.L.; Bradley, A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 2004, 14, 1902-1910.
38. Kapranov, P.; Cheng, J.; Dike, S.; Nix, D.A.; Duttagupta, R.; Willingham, A.T.; Stadler, P.F.; Hertel, J.; Hackermuller, J.; Hofacker, I.L. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316, 1484-1488.
39. Ogawa, Y.; Sun, B.K.; Lee, J.T. Intersection of the RNA interference and X-inactivation pathways. Science 2008, 320, 1336-1341.
40. Derrien, T.; Johnson, R.; Bussotti, G.; Tanzer, A.; Djebali, S.; Tilgner, H.; Guernec, G.; Martin, D.; Merkel, A.; Knowles, D.G. et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res.2012,22, 1775-1789.
41. Chen, Z.; Duan, X. Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications. Methods Mol. Biol. 2011, 733, 93-103.
42. Guttman, M.; Garber, M.; Levin, J.Z.; Donaghey, J.; Robinson, J.; Adiconis, X.; Fan, L.; Koziol, M.J.; Gnirke, A.; Nusbaum, C. et al. Ab. initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 2010, 28, 503-510.
43. Cabili, M.N.; Trapnell, C.; Goff, L.; Koziol, M.; Tazon-Vega, B.; Regev, A.; Rinn, J.L. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011, 25, 1915-1927.
44. Kutter, C.; Watt, S.; Stefflova, K.; Wilson, M.D.; Goncalves, A.; Ponting, C.P.; Odom, D.T.; Marques, A.C. Rapid turnover of long noncoding rnas and the evolution of gene expression. PLoS Genet. 2012, 8, e1002841.
45. ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447, 799-816.
46. Clark, M.B.; Amaral, P.P.; Schlesinger, F.J.; Dinger, M.E.; Taft, R.J.; Rinn, J.L.; Ponting, C.P.; Stadler, P.F.; Morris, K.V.; Morillon, A. et al. The reality of pervasive transcription. PLoS Biol. 2011, 9, doi:10.1371/journal.pbio.1000625.
47. Capel, B.; Swain, A.; Nicolis, S.; Hacker, A.; Walter, M.; Koopman, P.; Goodfellow, P.; Lovell-Badge, R. Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell 1993, 73, 1019-1030.
48. Cocquerelle, C.; Mascrez, B.; Hétuin, D.; Bailleul, B. Mis-splicing yields circular RNA molecules. FASEB J. 1993, 7, 155-160.
49. Nigro, J.M.; Cho, K.R.; Fearon, E.R.; Kern, S.E.; Ruppert, J.M.; Oliner, J.D.; Kinzler, K.W.; Vogelstein, B. Scrambled exons. Cell 1991, 64, 607-613.
50. Zaphiropoulos, P.G. Exon skipping and circular RNA formation in transcripts of the human cytochrome P-450 2C18 gene in epidermis and of the rat androgen binding protein gene in testis. Mol. Cell. Biol. 1997, 17, 2985-2993.
51. Memczak, S.; Jens, M.; Elefsinioti, A.; Torti, F.; Krueger, J.; Rybak, A.; Maier, L.; Mackowiak, S.D.; Gregersen, L.H.; Munschauer, M. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013, 495, 333-338.
52. Hansen, T.B.; Jensen, T.I.; Clausen, B.H.; Bramsen, J.B.; Finsen, B.; Damgaard, C.K.; Kjems, J. Natural RNA circles function as efficient microRNA sponges. Nature 2013, 495, 384-388.
53. Jeck, W.R.; Sorrentino, J.A.; Wang, K.; Slevin, M.K.; Burd, C.E.; Liu, J.; Marzluff, W.F.; Sharpless, N.E. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 2013, 19, 141-157.
54. Capriotti, E.; Marti-Renom, M.A. Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. BMC Bioinforma. 2010, 11, 322.
55. Rost, B. Twilight zone of protein sequence alignments. Protein Eng. 1999, 12, 85-94.
56. Pang, K.C.; Frith, M.C.; Mattick, J.S. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet. 2006, 22, 1-5.
57. Bernhart, S.H.; Hofacker, I.L. From consensus structure prediction to RNA gene finding. Brief Funct. Genomic Proteomic 2009, 8, 461-471.
58. Sun, Y.; Aljawad, O.; Lei, J.; Liu, A. Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy. BMC Bioinforma. 2012, 13, S12.
59. Bentwich, I.; Avniel, A.; Karov, Y.; Aharonov, R.; Gilad, S.; Barad, O.; Barzilai, A.; Einat, P.; Einav, U.; Meiri, E. et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 2005, 37, 766-770.
60. Berezikov, E.; van Tetering, G.; Verheul, M.; van de Belt, J.; van Laake, L.; Vos, J.; Verloop, R.; van de Wetering, M.; Guryev, V.; Takada, S. et al. Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res. 2006, 16, 1289-1298.
61. Guerra-Assuncao, J.A.; Enright, A.J. Large-scale analysis of microRNA evolution. BMC Genomics 2012, 13, 218.
62. Missal, K.; Rose, D.; Stadler, P.F. Non-coding RNAs in Ciona intestinalis. Bioinformatics 2005, 21, ii77-ii78.
63. Lindgreen, S.; Gardner, P.P.; Krogh, A. MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics 2007, 23, 3304-3311
64. Sperschneider, J.; Datta, A.; Wise, M.J. Predicting pseudoknotted structures across two RNA sequences. Bioinformatics 2012, 28, 3058-3065.
65. Wong, T.K.F.; Wan, K.-L.; Hsu, B.-Y.; Cheung, B.W.Y.; Hon, W.-K.; Lam, T.-W.; Yiu, S.-M. RNASAlign: RNA structural alignment system. Bioinformatics 2011, 27, 2151-2152.
66. Gardner, P.P.; Giegerich, R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinforma. 2004, 5, 140.
67. Ravindran, P.P.; Heroux, A.; Ye, J.D. Improvement of the crystallizability and expression of an RNA crystallization chaperone. J. Biochem. 2011, 150, 535-543.
68. Furtig, B.; Richter, C.; Wohnert, J.; Schwalbe, H. NMR spectroscopy of RNA. Chembiochem 2003, 4, 936-962.
69. Tzakos, A.G.; Grace, C.R.; Lukavsky, P.J.; Riek, R. NMR techniques for very large proteins and rnas in solution. Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 319-342.
70. Zuker, M.; Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981, 9, 133-148.
71. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31, 3406-3415.
72. Mathews, D.H.; Turner, D.H.; Zuker, M. RNA secondary structure prediction. Curr. Protoc. Nucleic Acid Chem. 2007, doi:10.1002/0471142700.nc1102s28.
73. Dowell, R.D.; Eddy, S.R. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinforma. 2004, 5, 71.
74. Dima, R.I.; Hyeon, C.; Thirumalai, D. Extracting stacking interaction parameters for RNA from the data set of native structures. J. Mol. Biol. 2005, 347, 53-69.
75. Do, C.B.; Woods, D.A.; Batzoglou, S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 2006, 22, e90-e98.
76. Xia, T.; SantaLucia, J.J.; Burkard, M.E.; Kierzek, R.; Schroeder, S.J.; Jiao, X.; Cox, C.; Turner, D.H. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 1998, 37, 14719-14735.
77. Mathews, D.H.; Sabina, J.; Zuker, M.; Turner, D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 1999, 288, 911-940.
78. Mathews, D.H.; Disney, M.D.; Childs, J.L.; Schroeder, S.J.; Zuker, M.; Turner, D.H. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 2004, 101, 7287-7292.
79. Lu, Z.J.; Turner, D.H.; Mathews, D.H. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res.2006,34, 4912-4924.
80. Lu, Z.J.; Gloor, J.W.; Mathews, D.H. Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA 2009, 15, 1805-1813.
81. Hofacker, I.L.; Fontana W.; Stadler, P.F.; Bonhoeffer S.; Tacker M.; Schuster, P. Fast folding and comparison of rna secondary structures. Monatshefte f. Chem. 1994, 125, 167-188.
82. McCaskill, J.S. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 1990, 29, 1105-1119.
83. Durbin, R.; Eddy, S.R.; Krogh, A.; Mitchison, G. Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids; Cambridge University Press: Cambridge, UK, 1998.
84. Deigan, K.E.; Li, T.W.; Mathews, D.H.; Weeks, K.M. Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. USA 2009, 106, 97-102.
85. Doshi, K.J.; Cannone, J.J.; Cobaugh, C.W.; Gutell, R.R. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinforma. 2004, 5, 105.
86. Herschlag, D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 1995, 270, 20871-20874.
87. Brennicke, A.; Marchfelder, A.; Binder, S. RNA editing. FEMS Microbiol. Rev. 1999, 23, 297-316.
88. Pan, T.; Sosnick, T. RNA folding during transcription. Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 161-175.
89. Mandal, M.; Breaker, R.R. Gene regulation by riboswitches. Nat. Rev. Mol. Cell. Biol. 2004, 5, 451-463.
90. Soukup, J.K.; Soukup, G.A. Riboswitches exert genetic control through metabolite-induced conformational change. Curr. Opin. Struct. Biol. 2004, 14, 344-349.
91. Bengert, P.; Dandekar, T. Riboswitch finder-A tool for identification of riboswitch RNAs. Nucleic Acids Res. 2004, 32, W154-W159.
92. Voss, B.; Meyer, C.; Giegerich, R. Evaluating the predictability of conformational switching in RNA. Bioinformatics 2004, 20, 1573-1582.
93. Hofacker, I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 2003, 31, 3429-3431.
94. Sankoff, D. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math. 1985, 45, 810-825.
95. Torarinsson, E.; Lindgreen, S. WAR: Webserver for aligning structural RNAs. Nucleic Acids Res. 2008, 36, W79-W84.
96. Bremges, A.; Schirmer, S.; Giegerich, R. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinforma. 2010, 11, 222.
97. Thompson, J.D.; Higgins, D.G.; Gibson, T.J. 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, 4673-4680.
98. Notredame, C.; Higgins, D.G.; Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000, 302, 205-217.
99. Hofacker, I.L.; Fekete, M.; Stadler, P.F. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 2002, 319, 1059-1066.
100. Knudsen, B.; Hein, J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 2003, 31, 3423-3428.
101. Ruan, J.; Stormo, G.D.; Zhang, W. An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics 2004, 20, 58-66.
102. Luck, R.; Graf, S.; Steger, G. ConStruct: A tool for thermodynamic controlled prediction of conserved secondary structure. Nucleic Acids Res. 1999, 27, 4208-4217.
103. Mathews, D.H.; Turner, D.H. Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol. 2002, 317, 191-203.
104. Mathews, D.H. Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics 2005, 21, 2246-2253.
105. Gorodkin, J.; Heyer, L.J.; Stormo, G.D. Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res. 1997, 25, 3724-3732.
106. Havgaard, J.H.; Lyngso, R.B.; Stormo, G.D.; Gorodkin, J. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 2005, 21, 1815-1824.
107. Holmes, I. Accelerated probabilistic inference of RNA structure evolution. BMC Bioinforma. 2005, 6, 73.
108. Dowell, R.D.; Eddy, S.R. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinforma. 2006, 7, 400.
109. Hofacker, I.L.; Bernhart, S.H.; Stadler, P.F. Alignment of RNA base pairing probability matrices. Bioinformatics 2004, 20, 2222-2227.
110. Wilm, A.; Higgins, D.G.; Notredame, C. R-Coffee: A method for multiple alignment of non-coding RNA. Nucleic Acids Res. 2008, 36, e52.
111. Reeder, J.; Giegerich, R. Consensus shapes: An alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics 2005, 21, 3516-3523.
112. Bernhart, S.H.; Hofacker, I.L.; Stadler, P.F. Local RNA base pairing probabilities in large sequences. Bioinformatics 2006, 22, 614-615.
113. Capriotti, E.; Marti-Renom, M.A. RNA structure alignment by a unit-vector approach. Bioinformatics 2008, 24, i112-i118.
114. Ferre, F.; Ponty, Y.; Lorenz, W.A.; Clote, P. DIAL: A web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res. 2007, 35, W659-W668.
115. Wang, C.W.; Chen, K.T.; Lu, C.L. iPARTS: An improved tool of pairwise alignment of RNA tertiary structures. Nucleic Acids Res. 2010, 38, W340-W347.
116. Dror, O.; Nussinov, R.; Wolfson, H. ARTS: Alignment of RNA tertiary structures. Bioinformatics 2005, 21, ii47-ii53.
117. Chang, Y.F.; Huang, Y.L.; Lu, C.L. SARSA: A web tool for structural alignment of RNA using a structural alphabet. Nucleic Acids Res. 2008, 36, W19-W24.
118. Bauer, R.P.; Rother, K.P.; Moor, P.P.; Reinert, K.P.; Steinke, T.P.; Bujnicki, J.P.; Preissner, R.P. Fast structural alignment of biomolecules using a hash table, N-grams and string descriptors. Algorithms 2009, 2, 692-709.
119. Kirillova, S.; Tosatto, S.C.; Carugo, O. FRASS: The web-server for RNA structural comparison. BMC Bioinforma. 2010, 11, 327.
120. Freyhult, E.K.; Bollback, J.P.; Gardner, P.P. Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA. Genome Res. 2007, 17, 117-125.
121. Smith, T.F.; Waterman, M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147, 195-197.
122. Rognes, T. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinforma. 2011, 12, 221.
123. Lipman, D.J.; Pearson, W.R. Rapid and sensitive protein similarity searches. Science 1985, 227, 1435-1441.
124. Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403-410.
125. Eddy, S.R. Profile hidden Markov models. Bioinformatics 1998, 14, 755-763.
126. Weinberg, Z.; Ruzzo, W.L. Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics 2006, 22, 35-39.
127. Holmes, I. A probabilistic model for the evolution of RNA structure. BMC Bioinforma. 2004, 5, 166.
128. Notredame, C.; O'Brien, E.A.; Higgins, D.G. RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Res. 1997, 25, 4570-4580.
129. Eddy, S.R.; Durbin, R. RNA sequence analysis using covariance models. Nucleic Acids Res. 1994, 22, 2079-2088.
130. Eddy, S.R. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinforma. 2002, 3, 18.
131. Klein, R.J.; Eddy, S.R. RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinforma. 2003, 4, 44.
132. Griffiths-Jones, S.; Bateman, A.; Marshall, M.; Khanna, A.; Eddy, S.R. Rfam: An RNA family database. Nucleic Acids Res. 2003, 31, 439-441.
133. Finn, R.D.; Tate, J.; Mistry, J.; Coggill, P.C.; Sammut, S.J.; Hotz, H.R.; Ceric, G.; Forslund, K.; Eddy, S.R.; Sonnhammer, E.L. et al. The Pfam protein families database. Nucleic Acids Res. 2008, 36, D281-D288.
134. Griffiths-Jones, S.; Moxon, S.; Marshall, M.; Khanna, A.; Eddy, S.R.; Bateman, A. Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 2005, 33, D121-D124.
135. 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, e557-e565.
136. Gardner, P.P.; Daub, J.; Tate, J.G.; Nawrocki, E.P.; Kolbe, D.L.; Lindgreen, S.; Wilkinson, A.C.; Finn, R.D.; Griffiths-Jones, S.; Eddy, S.R. et al. Rfam: Updates to the RNA families database. Nucleic Acids Res. 2009, 37, D136-D140.
137. Roshan, U.; Chikkagoudar, S.; Livesay, D.R. Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. BMC Bioinforma. 2008, 9, 61.
138. Bussotti, G.; Raineri, E.; Erb, I.; Zytnicki, M.; Wilm, A.; Beaudoing, E.; Bucher, P.; Notredame, C. BlastR-Fast and accurate database searches for non-coding RNAs. Nucleic Acids Res. 2011, 39, 6886-6895.
139. Lander, E.S.; Linton, L.M.; Birren, B.; Nusbaum, C.; Zody, M.C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; FitzHugh, W. et al. Initial sequencing and analysis of the human genome. Nature 2001, 409, 860-921.
140. Venter, J.C.; Adams, M.D.; Myers, E.W.; Li, P.W.; Mural, R.J.; Sutton, G.G.; Smith, H.O.; Yandell, M.; Evans, C.A.; Holt, R.A. et al. The sequence of the human genome. Science 2001, 291, 1304-1351.
141. Aparicio, S.; Chapman, J.; Stupka, E.; Putnam, N.; Chia, J.M.; Dehal, P.; Christoffels, A.; Rash, S.; Hoon, S.; Smit, A. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2002, 297, 1301-1310.
142. Waterston, R.H.; Lindblad-Toh, K.; Birney, E.; Rogers, J.; Abril, J.F.; Agarwal, P.; Agarwala, R.; Ainscough, R.; Alexandersson, M.; An, P. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420, 520-562.
143. Schwartz, S.; Kent, W.J.; Smit, A.; Zhang, Z.; Baertsch, R.; Hardison, R.C.; Haussler, D.; Miller, W. Human-mouse alignments with BLASTZ. Genome Res. 2003, 13, 103-107.
144. Boguski, M.S.; Tolstoshev, C.M.; Bassett, D.E.J. Gene discovery in dbEST. Science 1994, 265, 1993-1994.
145. Dias Neto, E.; Correa, R.G.; Verjovski-Almeida, S.; Briones, M.R.; Nagai, M.A.; da Silva, W.J.; Zago, M.A.; Bordin, S.; Costa, F.F.; Goldman, G.H. et al. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc. Natl. Acad. Sci. USA 2000, 97, 3491-3496.
146. Gerhard, D.S.; Wagner, L.; Feingold, E.A.; Shenmen, C.M.; Grouse, L.H.; Schuler, G.; Klein, S.L.; Old, S.; Rasooly, R.; Good, P. et al. The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome Res. 2004, 14, 2121-2127.
147. Boguski, M.S.; Lowe, T.M.; Tolstoshev, C.M. dbEST-Database for "expressed sequence tags." Nat. Genet. 1993, 4, 332-333.
148. Adams, M.D.; Kelley, J.M.; Gocayne, J.D.; Dubnick, M.; Polymeropoulos, M.H.; Xiao, H.; Merril, C.R.; Wu, A.; Olde, B.; Moreno, R.F. et al. Complementary DNA sequencing: Expressed sequence tags and human genome project. Science 1991, 252, 1651-1656.
149. Bonaldo, M.F.; Lennon, G.; Soares, M.B. Normalization and subtraction: Two approaches to facilitate gene discovery. Genome Res. 1996, 6, 791-806.
150. Nagaraj, S.H.; Gasser, R.B.; Ranganathan, S. A hitchhiker's guide to expressed sequence tag (EST) analysis. Brief. Bioinforma. 2007, 8, 6-21.
151. Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5, 621-628.
152. Malone, J.H.; Oliver, B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol. 2011, 9, 34.
153. Eklund, A.C.; Turner, L.R.; Chen, P.; Jensen, R.V.; deFeo, G.; Kopf-Sill, A.R.; Szallasi, Z. Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat. Biotechnol. 2006, 24, 1071-1073.
154. Okoniewski, M.J.; Miller, C.J. Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinforma. 2006, 7, 276.
155. Casneuf, T.; van de Peer, Y.; Huber, W. In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinforma. 2007, 8, 461.
156. Cox, W.G.; Beaudet, M.P.; Agnew, J.Y.; Ruth, J.L. Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. Anal. Biochem. 2004, 331, 243-254.
157. Dombkowski, A.A.; Thibodeau, B.J.; Starcevic, S.L.; Novak, R.F. Gene-specific dye bias in microarray reference designs. FEBS Lett. 2004, 560, 120-124.
158. Rosenzweig, B.A.; Pine, P.S.; Domon, O.E.; Morris, S.M.; Chen, J.J.; Sistare, F.D. Dye bias correction in dual-labeled cDNA microarray gene expression measurements. Environ. Health Perspect. 2004, 112, 480-487.
159. Dobbin, K.K.; Kawasaki, E.S.; Petersen, D.W.; Simon, R.M. Characterizing dye bias in microarray experiments. Bioinformatics 2005, 21, 2430-2437.
160. Martin-Magniette, M.L.; Aubert, J.; Cabannes, E.; Daudin, J.J. Evaluation of the gene-specific dye bias in cDNA microarray experiments. Bioinformatics 2005, 21, 1995-2000.
161. Bertone, P.; Stolc, V.; Royce, T.E.; Rozowsky, J.S.; Urban, A.E.; Zhu, X.; Rinn, J.L.; Tongprasit, W.; Samanta, M.; Weissman, S. et al. Global identification of human transcribed sequences with genome tiling arrays. Science 2004, 306, 2242-2246.
162. Cheng, J.; Kapranov, P.; Drenkow, J.; Dike, S.; Brubaker, S.; Patel, S.; Long, J.; Stern, D.; Tammana, H.; Helt, G. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005, 308, 1149-1154.
163. Royce, T.E.; Rozowsky, J.S.; Bertone, P.; Samanta, M.; Stolc, V.; Weissman, S.; Snyder, M.; Gerstein, M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet. 2005, 21, 466-475.
164. Kapranov, P.; Willingham, A.T.; Gingeras, T.R. Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet. 2007, 8, 413-423.
165. Wang, Z.; Gerstein, M.; Snyder, M. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57-63.
166. Marioni, J.C.; Mason, C.E.; Mane, S.M.; Stephens, M.; Gilad, Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18, 1509-1517.
167. Fu, X.; Fu, N.; Guo, S.; Yan, Z.; Xu, Y.; Hu, H.; Menzel, C.; Chen, W.; Li, Y.; Zeng, R. et al. Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 2009, 10, 161.
168. Ozsolak, F.; Milos, P.M. RNA Sequencing: Advances, challenges and opportunities. Nat. Rev. Genet. 2011, 12, 87-98.
169. Velculescu, V.E.; Zhang, L.; Vogelstein, B.; Kinzler, K.W. Serial analysis of gene expression. Science 1995, 270, 484-487.
170. Harbers, M.; Carninci, P. Tag-based approaches for transcriptome research and genome annotation. Nat. Methods 2005, 2, 495-502.
171. Saha, S.; Sparks, A. B.; Rago, C.; Akmaev, V.; Wang, C.J.; Vogelstein, B.; Kinzler, K.W.; Velculescu, V.E. Using the transcriptome to annotate the genome. Nat. Biotechnol. 2002, 20, 508-512.
172. Gowda, M.; Jantasuriyarat, C.; Dean, R.A.; Wang, G.L. Robust-LongSAGE (RL-SAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant. Physiol. 2004, 134, 890-897.
173. Matsumura, H.; Ito, A.; Saitoh, H.; Winter, P.; Kahl, G.; Reuter, M.; Kruger, D.H.; Terauchi, R. SuperSAGE. Cell. Microbiol. 2005, 7, 11-18.
174. Brenner, S.; Johnson, M.; Bridgham, J.; Golda, G.; Lloyd, D.H.; Johnson, D.; Luo, S.; McCurdy, S.; Foy, M.; Ewan, M. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 2000, 18, 630-634.
175. Ng, P.; Wei, C.L.; Sung, W.K.; Chiu, K.P.; Lipovich, L.; Ang, C.C.; Gupta, S.; Shahab, A.; Ridwan, A.; Wong, C.H. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat. Methods 2005, 2, 105-111.
176. Schaefer, B.C. Revolutions in rapid amplification of cDNA ends: New strategies for polymerase chain reaction cloning of full-length cDNA ends. Anal. Biochem. 1995, 227, 255-273.
177. Kapranov, P.; Drenkow, J.; Cheng, J.; Long, J.; Helt, G.; Dike, S.; Gingeras, T.R. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 2005, 15, 987-997.
178. Olivarius, S.; Plessy, C.; Carninci, P. High-throughput verification of transcriptional starting sites by Deep-RACE. BioTechniques 2009, 46, 130-132.
179. Kodzius, R.; Kojima, M.; Nishiyori, H.; Nakamura, M.; Fukuda, S.; Tagami, M.; Sasaki, D.; Imamura, K.; Kai, C.; Harbers, M. et al. CAGE: Cap analysis of gene expression. Nat. Methods 2006, 3, 211-222.
180. Shiraki, T.; Kondo, S.; Katayama, S.; Waki, K.; Kasukawa, T.; Kawaji, H.; Kodzius, R.; Watahiki, A.; Nakamura, M.; Arakawa, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. USA 2003, 100, 15776-15781.
181. Mercer, T.R.; Gerhardt, D.J.; Dinger, M.E.; Crawford, J.; Trapnell, C.; Jeddeloh, J.A.; Mattick, J.S.; Rinn, J.L. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 2011, 30, 99-104.
182. Mathavan, S.; Lee, S.G.; Mak, A.; Miller, L.D.; Murthy, K.R.; Govindarajan, K.R.; Tong, Y.; Wu, Y.L.; Lam, S.H.; Yang, H. et al. Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet. 2005, 1, 260-276.
183. Wang, E.T.; Sandberg, R.; Luo, S.; Khrebtukova, I.; Zhang, L.; Mayr, C.; Kingsmore, S.F.; Schroth, G.P.; Burge, C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456, 470-476.
184. Graveley, B.R.; Brooks, A.N.; Carlson, J.W.; Duff, M.O.; Landolin, J.M.; Yang, L.; Artieri, C.G.; van Baren, M.J.; Boley, N.; Booth, B.W. et al. The developmental transcriptome of Drosophila melanogaster. Nature 2011, 471, 473-479.
185. Pang, K.C.; Stephen, S.; Dinger, M.E.; Engström, P.G.; Lenhard, B.; Mattick, J.S. RNAdb 2.0- An expanded database of mammalian non-coding RNAs. Nucleic Acids Res.2007,35, D178-D182.
186. Kin, T.; Yamada, K.; Terai, G.; Okida, H.; Yoshinari, Y.; Ono, Y.; Kojima, A.; Kimura, Y.; Komori, T.; Asai, K. fRNAdb: A platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res. 2007, 35, D145-D148.
187. Liu, C.; Bai, B.; Skogerbo, G.; Cai, L.; Deng, W.; Zhang, Y.; Bu, D.; Zhao, Y.; Chen, R. NONCODE: An integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 2005, 33, D112-D125.
188. Pruitt, K.D.; Tatusova, T.; Klimke, W.; Maglott, D.R. NCBI reference Sequences: Current status, policy and new initiatives. Nucleic Acids Res. 2009, 37, D32-D36.
189. Harrow, J.; Denoeud, F.; Frankish, A.; Reymond, A.; Chen, C.K.; Chrast, J.; Lagarde, J.; Gilbert, J.G.; Storey, R.; Swarbreck, D, et al. GENCODE: Producing a reference annotation for ENCODE. Genome Biol. 2006, 7, S4 1-S4 9.
190. Havana team. Available online: http://www.sanger.ac.uk/research/projects/vertebrategenome/havana/ (accessed 6 March 2013).
191. Loveland, J.E.; Gilbert, J.G.; Griffiths, E.; Harrow, J.L. Community gene annotation in practice. Database (Oxford) 2012, 2012, doi:10.1093/database/bas009.
192. Flicek, P.; Amode, M.R.; Barrell, D.; Beal, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P.; Coates, G.; Fairley, S.; Fitzgerald, S. et al. Ensembl 2012. Nucleic Acids Res. 2012, 40, D84-D90.
193. Kawai, J.; Shinagawa, A.; Shibata, K.; Yoshino, M.; Itoh, M.; Ishii, Y.; Arakawa, T.; Hara, A.; Fukunishi, Y.; Konno, H. et al. Functional annotation of a full-length mouse cDNA collection. Nature 2001, 409, 685-690.
194. Pruitt, K.D.; Tatusova, T.; Brown, G.R.; Maglott, D.R. NCBI reference sequences (RefSeq): Current status, new features and genome annotation policy. Nucleic Acids Res.2012,40, D130-D135.
195. Kent, W.J.; Sugnet, C.W.; Furey, T.S.; Roskin, K.M.; Pringle, T.H.; Zahler, A.M.; Haussler, D. The human genome browser at UCSC. Genome Res. 2002, 12, 996-1006.
196. Stalker, J.; Gibbins, B.; Meidl, P.; Smith, J.; Spooner, W.; Hotz, H.R.; Cox, A.V. The Ensembl web site: Mechanics of a genome browser. Genome Res. 2004, 14, 951-955.
197. Wilming, L.G.; Gilbert, J.G.; Howe, K.; Trevanion, S.; Hubbard, T.; Harrow, J.L. The vertebrate genome annotation (Vega) database. Nucleic Acids Res. 2008, 36, D753-D760.
198. ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489, 57-74.
199. Martin, J.A.; Wang, Z. Next-generation transcriptome assembly. Nat. Rev. Genet. 2011, 12, 671-682.
200. Rogers, M.F.; Thomas, J.; Reddy, A.S.; Ben-Hur, A. SpliceGrapher: Detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol. 2012, 13, R4.
201. Metzker, M.L. Sequencing technologies-the next generation. Nat. Rev. Genet. 2010, 11, 31-46.
202. Butler, J.; MacCallum, I.; Kleber, M.; Shlyakhter, I.A.; Belmonte, M.K.; Lander, E.S.; Nusbaum, C.; Jaffe, D.B. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 2008, 18, 810-820.
203. Zerbino, D.R.; Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18, 821-829.
204. Simpson, J.T.; Wong, K.; Jackman, S.D.; Schein, J.E.; Jones, S.J.; Birol, I. ABySS: A parallel assembler for short read sequence data. Genome Res. 2009, 19, 1117-1123.
205. Li, R.; Li, Y.; Kristiansen, K.; Wang, J. SOAP: Short oligonucleotide alignment program. Bioinformatics 2008, 24, 713-714.
206. Lin, H.; Zhang, Z.; Zhang, M.Q.; Ma, B.; Li, M. ZOOM! Zillions of oligos mapped. Bioinformatics 2008, 24, 2431-2437.
207. Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10, R25.
208. Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25, 1754-1760.
209. Schatz, M.C. CloudBurst: Highly sensitive read mapping with MapReduce. Bioinformatics 2009, 25, 1363-1369.
210. Ahmadi, A.; Behm, A.; Honnalli, N.; Li, C.; Weng, L.; Xie, X. Hobbes: Optimized gram-based methods for efficient read alignment. Nucleic Acids Res. 2012, 40, e41.
211. Derrien, T.; Estelle, J.; Marco Sola, S.; Knowles, D.G.; Raineri, E.; Guigo, R.; Ribeca, P. Fast computation and applications of genome mappability. PLoS One 2012, 7, e30377.
212. Cloonan, N.; Xu, Q.; Faulkner, G.J.; Taylor, D.F.; Tang, D.T.; Kolle, G.; Grimmond, S.M. RNA-MATE: A recursive mapping strategy for high-throughput RNA-sequencing data. Bioinformatics 2009, 25, 2615-2616.
213. Trapnell, C.; Pachter, L.; Salzberg, S.L. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25, 1105-1111.
214. Li, H.; Ruan, J.; Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18, 1851-1858.
215. Smith, A.D.; Xuan, Z.; Zhang, M.Q. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinforma. 2008, 9, 128.
216. Ewing, B.; Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8, 186-194.
217. Ewing, B.; Hillier, L.; Wendl, M.C.; Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998, 8, 175-185.
218. Trapnell, C.; Williams, B.A.; Pertea, G.; Mortazavi, A.; Kwan, G.; van Baren, M.J.; Salzberg, S.L.; Wold, B.J.; Pachter, L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28, 511-515.
219. Li, W.; Feng, J.; Jiang, T. IsoLasso: A LASSO regression approach to RNA-Seq based transcriptome assembly. J. Comput. Biol. 2011, 18, 1693-1707.
220. Palmieri, N.; Nolte, V.; Suvorov, A.; Kosiol, C.; Schlötterer, C. Evaluation of different reference based annotation strategies using RNA-Seq-A case study in Drososphila pseudoobscura. PLoS One 2012, doi:10.1371/journal.pone.0046415.
221. Garg, R.; Patel, R.K.; Tyagi, A.K.; Jain, M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 2011, 18, 53-63.
222. Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644-652.
223. Jager, M.; Ott, C.E.; Grunhagen, J.; Hecht, J.; Schell, H.; Mundlos, S.; Duda, G.N.; Robinson, P.N.; Lienau, J. Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing. BMC Genomics 2011, 12, 158.
224. Keiler, K.C. Biology of trans-translation. Annu. Rev. Microbiol. 2008, 62, 133-151.
225. Novikova, I.V.; Hennelly, S.P.; Sanbonmatsu, K.Y. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res. 2012, 40, 5034-5051.
226. Clamp, M.; Fry, B.; Kamal, M.; Xie, X.; Cuff, J.; Lin, M.F.; Kellis, M.; Lindblad-Toh, K.; Lander, E.S. Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. USA 2007, 104, 19428-19433.
227. Lin, M.F.; Jungreis, I.; Kellis, M. PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 2011, 27, i275-i282.
228. Lin, M.F.; Carlson, J.W.; Crosby, M.A.; Matthews, B.B.; Yu, C.; Park, S.; Wan, K.H.; Schroeder, A.J.; Gramates, L.S.; St Pierre, S.E. et al. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res. 2007, 17, 1823-1836.
229. Liao, Q.; Liu, C.; Yuan, X.; Kang, S.; Miao, R.; Xiao, H.; Zhao, G.; Luo, H.; Bu, D.; Zhao, H. et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res. 2011, 39, 3864-3878.
230. Marchler-Bauer, A.; Panchenko, A.R.; Shoemaker, B.A.; Thiessen, P.A.; Geer, L.Y.; Bryant, S.H. CDD: A database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 2002, 30, 281-283.
231. UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012, 40, D71-D75.
232. Kong, L.; Zhang, Y.; Ye, Z.-Q.; Liu, X.-Q.; Zhao, S.-Q.; Wei, L.; Gao, G. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007, 35, W345-W349.
233. Arrial, R.T.; Togawa, R.C.; Brigido, M.M. Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: Case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinforma. 2009, 10, 239.
234. Wang, L.; Park, H.J.; Dasari, S.; Wang, S.; Kocher, J.-P.; Li, W. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013, 41, e74.
235. Mikkelsen, T.S.; Ku, M.; Jaffe, D.B.; Issac, B.; Lieberman, E.; Giannoukos, G.; Alvarez, P.; Brockman, W.; Kim, T.K.; Koche, R.P. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448, 553-560.
236. Lu, Z.J.; Yip, K.Y.; Wang, G.; Shou, C.; Hillier, L.W.; Khurana, E.; Agarwal, A.; Auerbach, R.; Rozowsky, J.; Cheng, C. et al. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res. 2011, 21, 276-285.
237. Esteve-Codina, A.; Kofler, R.; Palmieri, N.; Bussotti, G.; Notredame, C.; Perez-Enciso, M. Exploring the gonad transcriptome of two extreme male pigs with RNA-seq. BMC Genomics 2011, 12, 552.
238. Nam, J.W.; Bartel, D. Long non-coding RNAs in C. elegans. Genome Res. 2012, 22, 2529-2540.
239. Djebali, S.; Davis, C.A.; Merkel, A.; Dobin, A.; Lassmann, T.; Mortazavi, A.; Tanzer, A.; Lagarde, J.; Lin, W.; Schlesinger, F. et al. Landscape of transcription in human cells. Nature 2012, 489, 101-108.
240. Eveland, A.L.; McCarty, D.R.; Koch, K.E. Transcript profiling by3'-untranslated region sequencing resolves expression of gene families. Plant Physiol. 2008, 146, 32-44.
241. Hillier, L.W.; Reinke, V.; Green, P.; Hirst, M.; Marra, M.A.; Waterston, R.H. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 2009, 19, 657-666.
242. Nagalakshmi, U.; Wang, Z.; Waern, K.; Shou, C.; Raha, D.; Gerstein, M.; Snyder, M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320, 1344-1349.
243. Shendure, J. The beginning of the end for microarrays? Nat. Methods 2008, 5, 585-587.
244. Morozova, O.; Hirst, M.; Marra, M.A. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 2009, 10, 135-151.
245. Auer, P.L.; Doerge, R.W. Statistical design and analysis of RNA sequencing data. Genetics 2010, 185, 405-416.
246. Hiller, M.; Pudimat, R.; Busch, A.; Backofen, R. Using RNA secondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res. 2006, 34, e117.
247. Chang, T.-H.; Huang, H.-D.; Chuang, T.-N.; Shien, D.-M.; Horng, J.-T. RNAMST: Efficient and flexible approach for identifying RNA structural homologs. Nucleic Acids Res.2006,34, W423-W428.
248. Yao, Z.; Weinberg, Z.; Ruzzo, W.L. CMfinder-A covariance model based RNA motif finding algorithm. Bioinformatics 2006, 22, 445-452.
249. Ji, Y.; Xu, X.; Stormo, G.D. A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics 2004, 20, 1591-1602.
250. Riccitelli, N.J.; Lupták, A. Computational discovery of folded RNA domains in genomes and in vitro selected libraries. Methods 2010, 52, 133-140.
251. Gautheret, D.; Major, F.; Cedergren, R. Pattern searching/alignment with RNA primary and secondary structures: An effective descriptor for tRNA. Comput. Appl. Biosci. 1990, 6, 325-331.
252. Gautheret, D.; Lambert, A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J. Mol. Biol. 2001, 313, 1003-1011.
253. König, J.; Zarnack, K.; Luscombe, N.M.; Ule, J. Protein-RNA interactions: New genomic technologies and perspectives. Nat. Rev. Genet. 2011, 13, 77-83.
254. Rivas, E.; Eddy, S.R. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics 2000, 16, 583-605.
255. Kertesz, M.; Wan, Y.; Mazor, E.; Rinn, J.L.; Nutter, R.C.; Chang, H.Y.; Segal, E. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010, 467, 103-107.
256. Slater, G.S.; Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinforma. 2005, 6, 31.
257. Birney, E.; Clamp, M.; Durbin, R. GeneWise and genomewise. Genome Res. 2004, 14, 988-995.
258. Eyras, E.; Reymond, A.; Castelo, R.; Bye, J.M.; Camara, F.; Flicek, P.; Huckle, E.J.; Parra, G.; Shteynberg, D.D.; Wyss, C. et al. Gene finding in the chicken genome. BMC Bioinforma. 2005, 6, 131.
259. Mariotti, M.; Guigo, R. Selenoprofiles: Profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics 2010, 26, 2656-2663.
260. Vieira, F.G.; Rozas, J. Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: Origin and evolutionary history of the chemosensory system. Genome Biol. Evol. 2011, 3, 476-490.
261. Latos, P.A.; Pauler, F.M.; Koerner, M.V.; Şenergin, H.B.; Hudson, Q.J.; Stocsits, R.R.; Allhoff, W.; Stricker, S.H.; Klement, R.M.; Warczok, K.E. et al. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 2012, 338, 1469-1472.
262. Santoro, F.; Pauler, F.M. Silencing by the imprinted Airn macro lncRNA: Transcription is the answer. Cell. Cycle 2013, 12, 711-712.