RNAlien - Unsupervised RNA family model construction

Nucleic Acids Research

Volumn 44, Issue 17, 2016, Pages 8433-8441

  Eggenhofer, Florian ^a,b   Hofacker, Ivo L ^a   Höner Zu Siederdissen, Christian ^a,c  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF FREIBURG   (Germany)

^c UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER MODEL; CONTROLLED STUDY; GENE FUNCTION; GENE SEQUENCE; HUMAN; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; RNALIEN; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SOFTWARE; ALGORITHM; BASE PAIRING; CHEMISTRY; CONFORMATION; MOLECULAR MODEL; SEQUENCE HOMOLOGY; TIME FACTOR;

RNA;

ALGORITHMS; BASE PAIRING; HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; TIME FACTORS;

EID: 84991352111     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw558     Document Type: Article

References (36)

1. Mattick, J.S. and Makunin, I.V. (2006) Non-coding RNA. Hum. Mol. Genet., 15, R17-R29.
2. Hüttenhofer, A. and Vogel, J. (2006) Experimental approaches to identify non-coding RNAs. Nucleic Acids Res., 34, 635-646.
3. Washietl, S., Will, S., Hendrix, D.A., Goff, L.A., Rinn, J.L., Berger, B. and Kellis, M. (2012) Computational analysis of noncoding RNAs. Wiley Interdiscip. Rev., 3, 759-778.
4. Nawrocki, E.P., Kolbe, D.L. and Eddy, S.R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
5. Nawrocki, E.P. and Eddy, S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29, 2933-2935.
6. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. and Eddy, S.R. (2003) Rfam: an RNA family database. Nucleic Acids Res., 31, 439-441.
7. Gardner, P.P., Daub, J., Tate, J., Moore, B.L., Osuch, I.H., Griffiths-Jones, S., Finn, R.D., Nawrocki, E.P., Kolbe, D.L., Eddy, S.R. et al. (2011) Rfam:Wikipedia, clans and the 'decimal' release. Nucleic Acids Res., 39(Suppl. 1), D141-D145.
8. Menzel, P., Gorodkin, J. and Stadler, P.F. (2009) The tedious task of finding homologous noncoding RNA genes. RNA, 15, 2075-2082.
9. Li, S.-C., Pan, C.-Y. and Lin, W.-C. (2006) Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genomics, 7, 1-11.
10. Stadler, P.F., Chen, J. J.-L., Hackermüller, J., Hoffmann, S., Horn, F., Khaitovich, P., Kretzschmar, A.K., Mosig, A., Prohaska, S.J., Qi, X. et al. (2009) Evolution of vault RNAs. Mol. Biol. Evol., 26, 1975-1991.
11. Gruber, A.R., Koper-Emde, D., Marz, M., Tafer, H., Bernhart, S., Obernosterer, G., Mosig, A., Hofacker, I.L., Stadler, P.F. and Benecke, B.-J. (2008) Invertebrate 7SK /textitsnRNAs. J. Mol. Evol., 66, 107-115.
12. Gruber, A.R., Kilgus, C., Mosig, A., Hofacker, I.L., Hennig, W. and Stadler, P.F. (2008) Arthropod 7SKRNA. Mol. Biol. Evol., 25, 1923-1930.
13. Boria, I., Gruber, A.R., Tanzer, A., Bernhart, S.H., Lorenz, R., Mueller, M.M., Hofacker, I.L. and Stadler, P.F. (2010) Nematode sbRNAs: homologs of vertebrate YRNAs. J. Mol. Evol., 70, 346-358.
14. Nawrocki, E.P., Burge, S.W., Bateman, A., Daub, J., Eberhardt, R.Y., Eddy, S.R., Floden, E.W., Gardner, P.P., Jones, T.A., Tate, J. et al. (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res., 43, D130-D137.
15. Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
16. Lagesen, K., Hallin, P., Rødland, E., Stærfeldt, H., Rognes, T. and Ussery, D. (2007) RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res., 35, 3100-3108.
17. Lowe, T.M. and Eddy, S.R. (1999) A computational screen for methylation guide snoRNAs in yeast. Science, 283, 1168-1171.
18. Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S. et al. (2007) Database resources of the national center for biotechnology information. Nucleic Acids Res., 35(Suppl. 1), D5-D12.
19. Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F. and Backofen, R. (2007) Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput. Biol., 3, e65.
20. Gruber, A.R., Findeiß, S., Washietl, S., Hofacker, I.L. and Stadler, P.F. (2010) RNAz 2.0: Improved noncoding RNA detection. In: Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela, Hawaii, USA, 4-8 January 2010. pp. 69-79.
21. Sokal, R. and Michener, C. (1958) A statistical method for evaluating systematic relationships.Univ. Kans. Sci. Bull., 38, 1409-1438.
22. Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J. et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol., 7, 1-6.
23. Bernhart, S.H., Hofacker, I.L., Will, S., Gruber, A.R. and Stadler, P.F. (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474-487.
24. Washietl, S., Findeiß, S., Müller, S.A., Kalkhof, S., von Bergen, M., Hofacker, I.L., Stadler, P.F. and Goldman, N. (2011) RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA, 17, 578-594.
25. Bateman, A., Agrawal, S., Birney, E., Bruford, E.A., Bujnicki, J.M., Cochrane, G., Cole, J.R., Dinger, M.E., Enright, A.J., Gardner, P.P. et al. (2011) RNAcentral: a vision for an international database of RNA sequences. RNA, 17, 1941-1946.
26. Consortium, RNA (2014) RNAcentral: an international database of ncRNA sequences. Nucleic Acids Res., 43, D123-D129.
27. Benson, D.A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2011) GenBank. Nucleic Acids Res., 39, D32-D37.
28. Yates, A., Akanni, W., Amode, M.R., Barrell, D., Billis, K., Carvalho-Silva, D., Cummins, C., Clapham, P., Fitzgerald, S., Gil, L. et al. (2016) Ensembl 2016. Nucleic Acids Res., 44, D710-D716.
29. Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos-Zavaleta, A., Muñiz-Rascado, L., García-Sotelo, J.S., Weiss, V., Solano-Lira, H., Martínez-Flores, I., Medina-Rivera, A. et al. (2013) RegulonDB v8. 0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res., 41, D203-D213.
30. Wheeler, T.J. and Eddy, S.R. (2013) nhmmer: DNA homology search with profile HMMs. Bioinformatics, 29, 2487-2489.
31. Lorenz, R., Bernhart, S. H.F., zu Siederdissen, C.H., Tafer, H., Flamm, C., Stadler, P.F. and Hofacker, I.L. (2011) ViennaRNA Package 2.0. Algorithms Mol. Biol., 6, 26-40.
32. Wheeler, T.J., Clements, J., Eddy, S.R., Hubley, R., Jones, T.A., Jurka, J., Smit, A.F. and Finn, R.D. (2013) Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res., 41, D70-D82.
33. Pichon, X., Wilson, L.A., Stoneley, M., Bastide, A., King, H.A., Somers, J. andWillis, A.E. (2012) RNA binding protein/RNA element interactions and the control of translation. Curr. Protein Pept. Sci., 13, 294-304.
34. Eggenhofer, F., Hofacker, I.L. and zu Siederdissen, C.H. (2013) CMCompare webserver: comparing RNA families via covariance models. Nucleic Acids Res., 41, 499-503.
35. Höner zu Siederdissen, C. and Hofacker, I.L. (2010) Discriminatory power of RNA family models. Bioinformatics, 26, i453-i459.
36. Janssen, S. and Giegerich, R. (2015) Ambivalent covariance models. BMC Bioinformatics, 16, 178-195.