Predicting non-coding RNA transcripts

Bioinformatics: Tools and Applications

Volumn , Issue , 2007, Pages 65-97

  Kavanaugh, Laura A ^a   Ohler, Uwe ^a  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84900933768     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-92738-1_4     Document Type: Chapter

References (175)

1. Allmang C, Kufel J, Chanfreau G, Mitchell P, Petfalski E, Tollervey D (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J 18(19):5399-5410
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410
3. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H et al (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11(12):941-950
4. Aspinall T V, Gordon JM, Bennett HJ, Karahalios P, Bukowski JP, Walker SC et al (2007) Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNase P/MRP architecture. Nucleic Acids Res 35(19):6439-6450
5. Babak T, Blencowe BJ, Hughes TR (2005) A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 6:104
6. Bachellerie JP, Cavaille J, Huttenhofer A (2002) The expanding snoRNA world. Biochimie 84(8): 775-790
7. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2): 281-297
8. Bauer M, Klau GW, Reinert K (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinform 8:271
9. Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Dev 19(14):1635-1655
10. Bindewald E, Shapiro BA (2006) RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA 12(3):342-352
11. Bonnet E, Wuyts J, Rouze P, Van de Peer Y (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20(17):2911-2917
12. Brannan CI, Bartolomei MS (1999) Mechanisms of genomic imprinting. Curr Opin Genet Dev 9(2):164-170
13. Caprara MG, Nilsen TW (2000) RNA: versatility in form and function. Nat Struct Biol 7(10): 831-833
14. Carter RJ, Dubchak I, Holbrook SR (2001) A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res 29(19):3928-3938
15. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D et al (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116(4):499-509
16. Chen JH, Le S Y, Shapiro B, Currey KM, Maizel JV (1990) A computational procedure for assessing the significance of RNA secondary structure. Comput Appl Biosci 6(1):7-18
17. Chen JL, Blasco MA, Greider CW (2000) Secondary structure of vertebrate telomerase RNA. Cell 100(5):503-514
18. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S et al (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308(5725):1149-1154
19. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG et al (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31(13):3497-3500
20. Chiu DK, Kolodziejczak T (1991) Inferring consensus structure from nucleic acid sequences. Comput Appl Biosci 7(3):347-352
21. Chomsky N (1956) Three models for the description of language. IRE Transactions on Information Theory 2:113-124
22. Chomsky N (1959) On certain formal properties of grammers. Information and control 2(2):137-167
23. Clote P, Ferre F, Kranakis E, Krizanc D (2005) Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11(5):578-591
24. Costa FF (2007) Non-coding RNAs: lost in translation? Gene 386(1-2):1-10
25. Dann CE III, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winkler WC (2007) Structure and mechanism of a metal-sensing regulatory RNA. Cell 130(5):878-892
26. Decatur WA, Fournier MJ (2002) rRNA modifications and ribosome function. Trends Biochem Sci 27(7):344-351
27. Ding Y, Lawrence CE (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31(24):7280-7301
28. Ding Y, Chan C Y, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32(Web Server issue):W135-W141
29. Doshi KJ, Cannone JJ, Cobaugh CW, Gutell RR (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinform 5:105
30. Dowell RD, Eddy SR (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinform 7:400
31. Durbin R, Eddy SR, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids
32. Eddy SR (1996) Hidden Markov models. Curr Opin Struct Biol 6(3):361-365
33. Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2(12):919-929
34. Eddy SR (2002) A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinform 3:18
35. Edvardsson S, Gardner PP, Poole AM, Hendy MD, Penny D, Moulton V (2003) A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics 19(7):865-873
36. Frank DN, Pace NR (1998) Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem 67:153-180
37. Freyhult E, Gardner PP, Moulton V (2005) A comparison of RNA folding measures. BMC Bioinform 6:241
38. Freyhult EK, Bollback JP, Gardner PP (2007) Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res 17(1):117-125
39. Gardner PP, Giegerich R (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinform 5:140
40. Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 33(8):2433-2439
41. Gesteland RF, Cech TR, Atkins JF (2006) The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
42. Gillet R, Felden B (2001) Emerging views on tmRNA-mediated protein tagging and ribosome rescue. Mol Microbiol 42(4):879-885
43. Goodenbour JM, Pan T (2006) Diversity of tRNA genes in eukaryotes. Nucleic Acids Res 34(21):6137-6146
44. Gorodkin J, Heyer LJ, Brunak S, Stormo GD (1997) Displaying the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci 13(6):583-586
45. Gottesman S (2004) The small RNA regulators of Escherichia coli: roles and mechanisms*. Annu Rev Microbiol 58:303-328
46. Griffiths-Jones S (2005) RALEE-RNA ALignment editor in Emacs. Bioinformatics 21(2):257-259
47. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31(1):439-441
48. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33(Database issue):D121-D124
49. Gutell RR (1993) Collection of small subunit (16S-and 16S-like) ribosomal RNA structures. Nucleic Acids Res 21(13):3051-3054
50. Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD (1992) Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res 20(21):5785-5795
51. Hannon GJ, Rossi JJ (2004) Unlocking the potential of the human genome with RNA interference. Nature 431(7006):371-378
52. Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J (2005a) Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 21(9):1815-1824
53. Havgaard JH, Lyngso RB, Gorodkin J (2005a) The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res 33(Web Server issue):W650-W653
54. Hayashita Y, Osada H, Tatematsu Y, Yamada H, Yanagisawa K, Tomida S et al (2005) A polycis-tronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 65(21):9628-9632
55. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S et al (2005) A microRNA polycistron as a potential human oncogene. Nature 435(7043):828-833
56. Hershberg R, Altuvia S, Margalit H (2003) A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res 31(7):1813-1820
57. Hertel J, Hofacker IL, Stadler PF (2008) SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24(2):158-164
58. Higgs PG (2000) RNA secondary structure: physical and computational aspects. Q Rev Biophys 33(3):199-253
59. Hiley SL, Babak T, Hughes TR (2005a) Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5¢ end processing and tRNA splicing. Nucleic Acids Res 33(9):3048-3056
60. Hiley SL, Jackman J, Babak T, Trochesset M, Morris QD, Phizicky E et al (2005b) Detection and discovery of RNA modifications using microarrays. Nucleic Acids Res 33(1):e2
61. Hochsmann M, Voss B, Giegerich R (2004) Pure multiple RNA secondary structure alignments: a progressive profile approach. IEEE/ACM Trans Comput Biol Bioinform 1(1):53-62
62. Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31(13): 3429-3431
63. Hofacker IL (2007) RNA consensus structure prediction with RNAalifold. Methods Mol Biol 395:527-544
64. Hofacker IL, Fekete M, Stadler PF (2002) Secondary structure prediction for aligned RNA sequences. J Mol Biol 319(5):1059-1066
65. Holbrook SR (2005) RNA structure: the long and the short of it. Curr Opin Struct Biol 15(3):302-308
66. Holmes I (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinform 6:73
67. Huttenhofer A, Vogel J (2006) Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 34(2):635-646
68. Huttenhofer A, Schattner P, Polacek N (2005) Non-coding RNAs: hope or hype? Trends Genet 21(5):289-297
69. Hutvagner G, Simard MJ (2008) Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 9(1):22-32
70. Jones SJ (2006) Prediction of genomic functional elements. Annu Rev Genomics Hum Genet 7:315-338
71. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S et al (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 14(3):331-342
72. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP et al (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296(5569):916-919
73. Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S et al (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 15(7):987-997
74. Karlin S, Campbell AM, Mrazek J (1998) Comparative DNA analysis across diverse genomes. Annu Rev Genet 32:185-225
75. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M et al (2005) Antisense transcription in the mammalian transcriptome. Science 309(5740):1564-1566
76. Kavanaugh LA, Dietrich FS (in press) Non-coding RNA prediction and verification in Saccharomyces cerevisiae. PLoS Genet 5(1):e1000321
77. Kawano M, Reynolds AA, Miranda-Rios J, Storz G (2005) Detection of 5¢-and 3¢-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res 33(3):1040-1050
78. Keenan RJ, Freymann DM, Stroud RM, Walter P (2001) The signal recognition particle. Annu Rev Biochem 70:755-775
79. Klein RJ, Eddy SR (2003) RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinform 4:44
80. Klein RJ, Misulovin Z, Eddy SR (2002) Noncoding RNA genes identified in AT-rich hyperther-mophiles. Proc Natl Acad Sci USA 99(11):7542-7547
81. Knudsen B, Hein J (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15(6):446-454
82. Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31(13):3423-3428
83. Lai EC (2004) Predicting and validating microRNA targets. Genome Biol 5(9):115
84. Laslett D, Canback B, Andersson S (2002) BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences. Nucleic Acids Res 30(15):3449-3453
85. Le SV, Chen JH, Currey KM, Maizel JV Jr (1988) A program for predicting significant RNA secondary structures. Comput Appl Biosci 4(1):153-159
86. Le S Y, Chen JH, Maizel JV (1989) Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses. Nucleic Acids Res 17(15):6143-6152
87. Leighton PA, Ingram RS, Eggenschwiler J, Efstratiadis A, Tilghman SM (1995) Disruption of imprinting caused by deletion of the H19 gene region in mice. Nature 375(6526):34-39
88. Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118(1):69-82
89. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW et al (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17(8):991-1008
90. Lindgreen S, Gardner PP, Krogh A (2007) MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics 23(24):3304-3311
91. Livny J, Waldor MK (2007) Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol 10(2):96-101
92. Livny J, Fogel MA, Davis BM, Waldor MK (2005) sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res 33(13):4096-4105
93. Livny J, Brencic A, Lory S, Waldor MK (2006) Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res 34(12):3484-3493
94. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955-964
95. Lowe TM, Eddy SR (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283(5405):1168-1171
96. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309(5740):1567-1569
97. Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 29(22):4724-4735
98. Martens JA, Laprade L, Winston F (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429(6991):571-574
99. Mathews DH, Turner DH (2002) Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol 317(2):191-203
100. Mathews DH, Turner DH (2006) Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol 16(3):270-278
101. Mattick JS (2004a) RNA regulation: a new genetics? Nat Rev Genet 5(4):316-323
102. Mattick JS (2004b) The hidden genetic program of complex organisms. Sci Am 291(4):60-67
103. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15(Spec No. 1):R17-R29
104. McCaskill JS (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105-1119
105. Meier UT (2005) The many facets of H/ACA ribonucleoproteins. Chromosoma 114(1):1-14
106. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431(7006):343-349
107. Mendes Soares LM, Valcarcel J (2006) The expanding transcriptome: the genome as the 'Book of Sand'. EMBO J 25(5):923-931
108. Meyer IM (2007) A practical guide to the art of RNA gene prediction. Brief Bioinform 8(6):396-414
109. Meyer IM, Miklos I (2004) Co-transcriptional folding is encoded within RNA genes. BMC Mol Biol 5:10
110. Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C (2007) The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res 35(Web Server issue):W645-W648
111. Neugebauer KM (2002) On the importance of being co-transcriptional. J Cell Sci 115(Pt 20):3865-3871
112. Nussinov R, Pieczenik G, Griggs JR, Kleitman DJ (1978) Algorithms for loop matchings. SIAM J Appl Math 35(1):68-82
113. Ogurtsov AY, Shabalina SA, Kondrashov AS, Roytberg MA (2006) Analysis of internal loops within the RNA secondary structure in almost quadratic time. Bioinformatics 22(11):1317-1324
114. Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB (2004) Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10(9):1309-1322
115. Olivas WM, Muhlrad D, Parker R (1997) Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs. Nucleic Acids Res 25(22):4619-4625
116. Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP (2000) Homologs of small nucleolar RNAs in Archaea. Science 288(5465):517-522
117. Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 132:185-219
118. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85(8):2444-2448
119. Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J (2004) A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res 32(16):4925-4936
120. Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES et al (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2(4):e33
121. Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q et al (2003) A panoramic view of yeast noncoding RNA processing. Cell 113(7):919-933
122. Pichon C, Felden B (2003) Intergenic sequence inspector: searching and identifying bacterial RNAs. Bioinformatics 19(13):1707-1709
123. Pichon C, Felden B (2005) Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci USA 102(40):14249-14254
124. Reeder J, Giegerich R (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinform 5:104
125. Reeder J, Giegerich R (2005) Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics 21(17):3516-3523
126. Reeder J, Hochsmann M, Rehmsmeier M, Voss B, Giegerich R (2006) Beyond Mfold: recent advances in RNA bioinformatics. J Biotechnol 124(1):41-55
127. Ren J, Rastegari B, Condon A, Hoos HH (2005) HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA 11(10):1494-1504
128. Repsilber D, Wiese S, Rachen M, Schroder AW, Riesner D, Steger G (1999) Formation of metastable RNA structures by sequential folding during transcription: time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis. RNA 5(4):574-584
129. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110(4):513-520
130. Rivas E, Eddy SR (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol 285(5):2053-2068
131. Rivas E, Eddy SR (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics 16(7):583-605
132. Rivas E, Eddy SR (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinform 2(1):8
133. Rivas E, Klein RJ, Jones TA, Eddy SR (2001) Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 11(17):1369-1373
134. Ruan J, Stormo GD, Zhang W (2004a) An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics 20(1):58-66
135. Ruan J, Stormo GD, Zhang W (2004b) ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res 32(Web Server issue):W146-W149
136. Saguy M, Gillet R, Metzinger L, Felden B (2005) tmRNA and associated ligands: a puzzling relationship. Biochimie 87(9-10):897-903
137. Samanta MP, Tongprasit W, Sethi H, Chin CS, Stolc V (2006) Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proc Natl Acad Sci USA 103(11):4192-4197
138. Sankoff D (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J Appl Math 45:810-825
139. Schattner P (2002) Searching for RNA genes using base-composition statistics. Nucleic Acids Res 30(9):2076-2082
140. Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM (2004) Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res 32(14):4281-4296
141. Seitz H, Youngson N, Lin SP, Dalbert S, Paulsen M, Bachellerie JP et al (2003) Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat Genet 34(3):261-262
142. Siebert S, Backofen R (2007) Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA. Methods Mol Biol 395:489-502
143. Sonkoly E, Bata-Csorgo Z, Pivarcsi A, Polyanka H, Kenderessy-Szabo A, Molnar G et al (2005) Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS. J Biol Chem 280(25):24159-24167
144. Sontheimer EJ, Carthew RW (2005) Silence from within: endogenous siRNAs and miRNAs. Cell 122(1):9-12
145. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26(1):148-153
146. Stark BC, Kole R, Bowman EJ, Altman S (1978) Ribonuclease P: an enzyme with an essential RNA component. Proc Natl Acad Sci USA 75(8):3717-3721
147. Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics 22(4):500-503
148. Storz G (2002) An expanding universe of noncoding RNAs. Science 296(5571):1260-1263
149. Storz G, Opdyke JA, Zhang A (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 7(2):140-144
150. Terai G, Komori T, Asai K, Kin T (2007) miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. RNA 13(12):2081-2090
151. Tilghman SM (1999) The sins of the fathers and mothers: genomic imprinting in mammalian development. Cell 96(2):185-193
152. Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J (2006) Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res 16(7):885-889
153. Torarinsson E, Havgaard JH, Gorodkin J (2007) Multiple structural alignment and clustering of RNA sequences. Bioinformatics 23(8):926-932
154. Venema J, Tollervey D (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311
155. Verdel A, Moazed D (2005) RNAi-directed assembly of heterochromatin in fission yeast. FEBS Lett 579:5872-5878
156. Voss B (2006) Structural analysis of aligned RNAs. Nucleic Acids Res 34(19):5471-5481
157. Wang XJ, Reyes JL, Chua NH, Gaasterland T (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 5(9):R65
158. Washietl S, Hofacker IL (2004) Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 342(1):19-30
159. Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF (2005a) Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol 23(11):1383-1390
160. Washietl S, Hofacker IL, Stadler PF (2005b) Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA 102(7):2454-2459
161. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermuller J et al (2007) Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 17(6):852-864
162. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15(13):1637-1651
163. Wilderman PJ, Sowa NA, FitzGerald DJ, FitzGerald PC, Gottesman S, Ochsner UA et al (2004) Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc Natl Acad Sci USA 101(26):9792-9797
164. Witwer C, Hofacker IL, Stadler PF (2004) Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans Comput Biol Bioinform 1(2):66-77
165. Workman C, Krogh A (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res 27(24):4816-4822
166. Wuchty S, Fontana W, Hofacker IL, Schuster P (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49(2):145-165
167. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K et al (2005) Systematic discovery of regulatory motifs in human promoters and 3¢ UTRs by comparison of several mammals. Nature 434(7031):338-345
168. Xu X, Ji Y, Stormo GD (2007) RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics 23(15):1883-1891
169. Yao Z, Weinberg Z, Ruzzo WL (2006) CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics 22(4):445-452
170. Yin JQ, Zhao RC (2007) Identifying expression of new small RNAs by microarrays. Methods 43(2):123-130
171. Zamore PD, Haley B (2005) Ribo-gnome: the big world of small RNAs. Science 309(5740): 1519-1524
172. Zhang Y, Zhang Z, Ling L, Shi B, Chen R (2004) Conservation analysis of small RNA genes in Escherichia coli. Bioinformatics 20(5):599-603
173. Zuker M (1989) Computer prediction of RNA structure. Methods Enzymol 180:262-288
174. Zuker M, Sankoff D (1984) RNA secondary structures and their prediction. Bull Math Biol 46:591-621
175. Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9(1):133-148