DiProDB: A database for dinucleotide properties

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Friedel, Maik ^a   Nikolajewa, Swetlana ^b   Sühnel, Jürgen ^a   Wilhelm, Thomas ^c  

^a FRITZ LIPMANN INSTITUTE   (Germany)

^b FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^c INSTITUTE OF FOOD RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; SINGLE STRANDED DNA; SINGLE STRANDED RNA;

ARTICLE; COMPUTER INTERFACE; CONFORMATIONAL TRANSITION; CONTENT ANALYSIS; CORRELATION ANALYSIS; DATA ANALYSIS; GENE CLUSTER; INTERNET; LINKAGE ANALYSIS; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEIC ACID DATABASE; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; THERMODYNAMICS;

DATABASES, NUCLEIC ACID; DINUCLEOSIDE PHOSPHATES; DNA; NUCLEIC ACID CONFORMATION; RNA; THERMODYNAMICS; USER-COMPUTER INTERFACE;

EID: 58149196205     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn597     Document Type: Article

References (15)

1. SantaLucia,J. Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbour thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
2. Mathews,D.H. and Turner,D.H. (2006) Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16, 270-278.
3. Goñi,J.R., Pérez,A., Torrents,D. and Orozco,M. (2007) Determining promoter location based on DNA structure first-principles calculations. Genome Biol., 8, R263.
4. Pérez-Martín,J., Rojo,F. and de Lorenzo,V. (1994) Promoters responsive to DNA bending: A common theme in prokaryotic gene expression. Microbiol. Rev., 58, 268-290.
5. Abeel,T., Saeys,Y., Rouze',P. and Van de Peer,Y. (2008) ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics, 24, i24-i31.
6. Florquin,K., Saeys,Y., Degroeve,S., Rouzé,P. and Van de Peer,Y. (2005) Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res., 33, 4255-4264.
7. Ponomarenko,J.V., Ponomarenko,M.P., Frolov,A.S., Vorobyev,D.G., Overton,G.C. and Kolchanov,N.A. (1999) Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics, 15, 654-668.
8. Nikolajewa,S., Beyer,A., Friedel,M., Hollunder,J. and Wilhelm,T. (2005) Common patterns in type II restriction enzyme binding sites. Nucleic Acids Res., 33, 2726-2733.
9. Karas,H., Knüppel,R., Schulz,W., Sklenar,H. and Wingender,E. (1996) Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements. Comput. Appl. Biosci. 12, 441-446.
10. Pérez,A., Noy,A., Lankas,F., Luque,F.J. and Orozco,M. (2004) The relative flexibility of B-DNA and A-RNA duplexes: Database analysis. Nucleic Acids Res., 32, 6144-6151.
11. Gorin,A.A., Zhurkin,V.B. and Olson,W.K. (1995) B-DNA twisting correlates with base-pair morphology. J. Mol. Biol., 247, 34-48.
12. Suzuki,M., Yagi,N. and Finch,J.T. (1996) Role of base-backbone and base-base interactions in alternating DNA conformations. FEBS Lett. 379, 148-152.
13. Shpigelman,E.S., Trifonov,E.N. and Bolshoy,A. (1993) CURVATURE: Software for the analysis of curved DNA. Comput. Appl. Biosci., 9, 435-440.
14. Ward,J.H. (1963) Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc., 58, 236-244.
15. Pearson,K. (1901) On lines and planes of closest fit to systems of points in space. Philos. Magazine, 2, 559-572.