Locomotif: From graphical motif description to RNA motif search

Bioinformatics

Volumn 23, Issue 13, 2007, Pages

  Reeder, Janina ^a   Reeder, Jens ^a   Giegerich, Robert ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

AUTOMATION; BACTERIAL GENETICS; BIOINFORMATICS; CLIENT SERVER APPLICATION; COMPUTER LANGUAGE; COMPUTER PROGRAM; CONFERENCE PAPER; CONTROLLED STUDY; ESCHERICHIA COLI; GENETIC ALGORITHM; INFORMATION RETRIEVAL; MOLECULAR SIZE; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; THERMODYNAMICS;

EID: 34547840236     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm179     Document Type: Conference Paper

References (26)

1. Argaman, L. and Altuvia, S. (2000) fhlA repression by OxyS RNA: Kissing complex formation at two sites results in a stable antisense-target RNAcomplex. J. Mol. Biol., 300, 1101-1112.
2. Billoud, B. et al. (1996) Palingol: A declarative programming language to describe nucleic acids secondary structures and to scan sequence databases. Nucleic Acids Res., 24, 1395-1403.
3. Burge, C. and Karlin, S. (1998) Finding the genes in genomic DNA. Curr. Opin. Struct. Biol., 8, 346-354.
4. Clote, P. et al. (2005) Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA, 11, 578-591.
5. Dsouza, M. et al. (1997) Searching for patterns in genomic data. TIG, 13, 497-498.
6. Giegerich, R. et al. (2004a) A discipline of dynamic programming over sequence data. Sci. Compu. Programm., 51, 215-265.
7. Giegerich, R. et al. (2004b) Abstract Shapes of RNA, Nucleic Acids Res., 32, 4843-4851.
8. Griffiths-Jones, S. et al. (2005) Rfam: Annotating non-coding RNAs in complete geuomes. Nucleic Acids Res., 33, D121-D124.
9. Höchsmann, T. et al. (2006) Thermodynamic matchers: strengthening the significance of RNA folding energies. In Computational Systems Bioinformatics, Proceedings of the Conference CSB 2006.
10. Hofacker, I.L. et al. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188.
11. Hüttenhofer, A. and Vögel, J. (2006) Experimental approaches to identify non-coding RNAs. Nucleic Acids Res., 34, 636-646.
12. Laferrière, A. et al. (1994) An RNA pattern matching program with enhanced performance and portability. Comput. Appl. Biosci., 10, 211-212.
13. Macke, T.J. et al. (2001) RNAMotof, an RNA secondary structure definition and search algorithm. Nucleic Acids Res., 29, 4724-4735.
14. Mathews, D. et al. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
15. McHardy, A. et al. (2004) Development of joint application strategies for two microbial gene finders. Bioinformatics, 20 1622-1631.
16. Pesole, G. et al. (2000) Patsearch: A pattern matcher software that finds functional elements in nucleotide and protein sequencers and assesses their statistical significance. Bioinformatics, 16, 439-450.
17. Reeder, J. (2007) Locomotif: A Graphical Programming System for RNA Motif Search. PhD Thesis, Technische Fakultät, Universität Bielefeld.
18. Reeder, J. and Giegerich, R. (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5.
19. Reeder, J. and Giegerich, R. (2006) A graphical programming system for molecular motif search. In GPCE '06: Proceedings of the 5th International Conference on Generative Programming and Component Engineering, ACM Press, New York, USA, pp. 131-140.
20. Rüberg, S. et al. (2003) Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: Genome-wide profiling of osmoadaptive gene expression. J. Biotechnol., 106 255-268.
21. Steffen, P. (2006) Compiling a Domain Specific Language for Dynamic Programming: Challenges and Solutions. PhD Thesis, Technische Fakultät, Universität Bielefeld.
22. Steffen, P. and Giegerich, R. (2005) Versatile and declarative dynamic programming using pair algebras. BMC Bioinformatics, 6.
23. Steffen, P. and Giegerich, R. (2006) Table design in dynamic programming. Inf. Computa., 204, 1325-1345.
24. Vogel, J. and Sharma, C. (2005) How to find small noncoding RNAs in bacteria. Biol. Chem., 386, 1219-1238.
25. Washietl, S. et al. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102, 2454-2459.
26. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.