chipD: A web tool to design oligonucleotide probes for high-density tiling arrays

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Dufour, Yann S ^a   Wesenberg, Gary E ^a   Tritt, Andrew J ^a   Glasner, Jeremy D ^a   Perna, Nicole T ^a   Mitchell, Julie C ^a   Donohue, Timothy J ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE LOCATION; GENE SEQUENCE; GENE TARGETING; GENETIC ALGORITHM; GENOMICS; HYBRIDIZATION; INTERNET; NONHUMAN; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; RHODOBACTER SPHAEROIDES; THERMODYNAMICS; ALGORITHM; CHEMISTRY; GENETICS;

ALGORITHMS; GENE EXPRESSION PROFILING; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; RHODOBACTER SPHAEROIDES; SOFTWARE; USER-COMPUTER INTERFACE;

OLIGONUCLEOTIDE PROBE;

EID: 77954280971     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq517     Document Type: Article

References (17)

1. Liu,X.S. (2007) Getting started in tiling microarray analysis. PLoS Comput. Biol., 3, 1842-1844.
2. Mockler,T.C., Chan,S., Sundaresan,A., Chen,H., Jacobsen,S.E. and Ecker,J.R. (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics, 85, 1-15.
3. Mei,R., Hubbell,E., Bekiranov,S., Mittmann,M., Christians,F.C., Shen,M.M., Lu,G., Fang,J., Liu,W.M., Ryder,T. et al. (2003) Probe selection for high-density oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 100, 11237-11242.
4. Chou,H.H., Hsia,A.P., Mooney,D.L. and Schnable,P.S. (2004) Picky: oligo microarray design for large genomes. Bioinformatics, 20, 2893-2902.
5. Li,X., He,Z. and Zhou,J. (2005) Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res., 33, 6114-6123.
6. Rouillard,J.M., Zuker,M. and Gulari,E. (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res., 31, 3057-3062.
7. Wernersson,R. and Nielsen,H.B. (2005) OligoWiz 2.0-integrating sequence feature annotation into the design of microarray probes. Nucleic Acids Res., 33, W611-W615.
8. Ryder,E., Jackson,R., Ferguson-Smith,A. and Russell,S. (2006) MAMMOT-a set of tools for the design, management and visualization of genomic tiling arrays. Bioinformatics, 22, 883-884.
9. Lipson,D., Yakhini,Z. and Aumann,Y. (2007) Optimization of probe coverage for high-resolution oligonucleotide aCGH. Bioinformatics, 23, e77-e83.
10. Graf,S., Nielsen,F.G., Kurtz,S., Huynen,M.A., Birney,E., Stunnenberg,H. and Flicek,P. (2007) Optimized design and assessment of whole genome tiling arrays. Bioinformatics, 23, i195-i204.
11. Bertone,P., Trifonov,V., Rozowsky,J.S., Schubert,F., Emanuelsson,O., Karro,J., Kao,M.Y., Snyder,M. and Gerstein,M. (2006) Design optimization methods for genomic DNA tiling arrays. Genome Res, 16, 271-281.
12. Lemoine,S., Combes,F. and Le Crom,S. (2009) An evaluation of custom microarray applications: the oligonucleotide design challenge. Nucleic Acids Res., 37, 1726-1739.
13. Wernersson,R., Juncker,A.S. and Nielsen,H.B. (2007) Probe selection for DNA microarrays using OligoWiz. Nat. Protoc., 2, 2677-2691.
14. SantaLucia,J. Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
15. Wetmur,J.G. (1991) DNA probes: applications of the principles of nucleic acid hybridization. Crit. Rev. Biochem. Mol. Biol., 26, 227-259.
16. Dufour,Y.S., Landick,R. and Donohue,T.J. (2008) Organization and evolution of the biological response to singlet oxygen stress. J. Mol. Biol., 383, 713-730.
17. Peters,J.M., Mooney,R.A., Kuan,P.F., Rowland,J.L., Keles,S. and Landick,R. (2009) Rho directs widespread termination of intragenic and stable RNA transcription. Proc. Natl Acad. Sci. USA, 106, 15406-15411.