Structural profiles of human miRNA families from pairwise clustering

Bioinformatics

Volumn 25, Issue 3, 2009, Pages 291-294

  Kaczkowski, Bogumił ^a   Torarinsson, Elfar ^a   Reiche, Kristin ^b   Havgaard, Jakob Hull ^a   Stadler, Peter F ^b,c,d,e   Gorodkin, Jan ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b FRAUNHOFER INSTITUTE FOR CELL THERAPY AND IMMUNOLOGY   (Germany)

^c UNIVERSITY OF LEIPZIG   (Germany)

^d SANTA FE INSTITUTE   (United States)

^e UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; BIOINFORMATICS; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONSENSUS SEQUENCE; DATA BASE; HUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 59549089683     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn628     Document Type: Article

References (30)

1. Duda,R.O. et al. (2001) Pattern Classification. John Wiley & Sons, Inc., New York.
2. Farazi,T.A. et al. (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development, 135, 1201-1214.
3. Förstemann,K. et al. (2007) Drosophila microRNAs are sorted into functionally distinct Argonaute complexes after production by Dicer-1. Cell, 130, 287-297.
4. Gorodkin,J. et al. (2006) MicroRNA sequence motifs reveal asymmetry between the stem arms. Comput. Biol. Chem., 30, 249-254.
5. Griffiths-Jones,S. et al. (2003) Rfam: An RNA family database. Nucleic Acids Res., 31, 439-441.
6. Griffiths-Jones,S. et al. (2006) miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, 1362-4962.
7. Havgaard,J.H. et al. (2007) Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol., 3, 1896-1908.
8. Hertel,J. et al. (2006) and The Students of Bioinformatics Computer Labs 2004 and 2005. The Expansion of the Metazoan MicroRNA Repertoire. BMC Genomics, 7, 15.
9. Ihaka,R. and Gentleman,R. (1996) R: A language for data analysis and graphics. J. Comput. Graph. Stat., 5, 299-314.
10. Kato,M. and Slack,F.J. (2008) MicroRNAs: Small molecules with big roles - C. elegans to human cancer. Biol. Cell, 100, 71-81.
11. Lewis,B.P. et al. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
12. Lindow,M. and Gorodkin,J. (2007) Principles and limitations of computational microRNA gene and target finding. DNA Cell Biol., 26, 339-351.
13. Maroney,P.A. et al. (2006) MicroRNAs, mRNAs, and translation. Cold Spring Harb. Symp. Quant. Biol., 71, 531-535.
14. Matthews,B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
15. Mette,M.F. et al. (2002) Short RNAs can identify new candidate transposable element families in arabidopsis. Plant Physiol., 130, 6-9.
16. Nawrocki,E.P. and Eddy,S.R. (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput. Biol., 3, e56.
17. Pearson,W.R. (1991) Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics, 11, 635-650.
18. Peters,L. and Meister,G. (2007) Argonaute proteins: Mediators of RNA silencing. Mol. Cell, 26, 611-623.
19. Piriyapongsa,J. and Jordan,K.I. (2007) A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS ONE, 2, e203.
20. Rabani,M. et al. (2008) Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc. Natl Acad. Sci. USA, 105, 14885-14890.
21. Ritchiel,W. et al. (2007) RNA stemloops: To be or not to be cleaved by RNAse III. RNA. RNA, 13, 457-462.
22. Sankoff,D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math., 45, 810-825.
23. Schmittgen,T.D. (2008) Regulation of microRNA processing in development, differentiation and cancer. J. Cell Mol. Med., 12, 1811-1819.
24. Schuster,P. et al. (1994) From sequences to shapes and back: A case study in RNA secondary structures. Proc. R. Soc. Lond. B, 255, 279-284.
25. Suzuki,M. and Hayashizaki,Y. (2004) Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs. Bioessays, 26, 833-843.
26. Suzuki,R. and Shimodaira,H. (2006) Pvclust: An R package for assessing the uncertainty in hierarchical clustering. Bioinformatics, 22 1540-1542.
27. Tomari,Y. et al. (2007) Sorting of Drosophila small silencing RNAs. Cell, 130, 299-308.
28. Torarinsson,E. and Lindgreen,S. (2008) WAR: Webserver for aligning structural RNAs. Nucleic Acids Res. of print, doi:10.1093/nar/gkn275, May 20, 2008.
29. Weinberg,Z. and Ruzzo,W.L. (2006) Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics., 22, 35-39.
30. Zhang,B. et al. (2006) MicroRNA: A new player in stem cells. J. Cell Physiol., 209, 266-269.