HiSpOD: Probe design for functional DNA microarrays

Bioinformatics

Volumn 27, Issue 5, 2011, Pages 641-648

  Dugat Bony, Eric ^a,b   Missaoui, Mohieddine ^a,c   Peyretaillade, Eric ^a,b   Biderre Petit, Corinne ^a,b   Bouzid, Ourdia ^a,b   Gouinaud, Christophe ^a,c   Hill, David ^a,c   Peyret, Pierre ^a,b  

^a UNIVERSITÉ CLERMONT AUVERGNE   (France)

^b UNIVERSITÉ BLAISE PASCAL   (France)

^c UNIVERSITÉ BLAISE PASCAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOREMEDIATION; BIOSYNTHESIS; COMPUTER PROGRAM; CONSENSUS SEQUENCE; DNA MICROARRAY; ENVIRONMENTAL MONITORING; METHODOLOGY; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT;

ALGORITHMS; BASE SEQUENCE; BIODEGRADATION, ENVIRONMENTAL; CONSENSUS SEQUENCE; DATABASES, NUCLEIC ACID; ENVIRONMENTAL MONITORING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 79951971276     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq712     Document Type: Article

References (37)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Arp,D.J. et al. (2001) Molecular and cellular fundamentals of aerobic cometabolism of trichloroethylene. Biodegradation, 12, 81-103.
3. Berthrong,S.T. et al. (2009) Afforestation alters the soil functional gene composition and biogeochemical processes in South American grasslands. Appl. Environ. Microbiol., 15, 6240-6248.
4. Bruun,G.M. et al. (2007) Improving comparability between microarray probe signals by thermodynamic intensity correction. Nucleic Acids Res., 35, e48.
5. Chung,W.-H. et al. (2005) Design of long oligonucleotide probes for functional gene detection in a microbial community. Bioinformatics, 21, 4092-4100.
6. Darling,A. et al. (2003) The design, implementation, and evaluation of mpiBLAST. In 4th International Conference on Linux Clusters: The HPC Revolution 2003. San Jose, California.
7. Feng,S. and Tillier,E.R.M. (2007) A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Bioinformatics, 23, 1195-1202.
8. Futagami,T. et al. (2008) Biochemical and genetic bases of dehalorespiration. Chem. Rec., 8, 1-12.
9. Gao,H. et al. (2007) Microarray-Based analysis of microbial community RNAs by whole-community RNA amplification. Appl. Environ. Microbiol., 73, 563-571.
10. Gentry,T. et al. (2006) Microarray applications in microbial ecology research. Microb. Ecol., 52, 159-175.
11. Habe,H. and Omori,T. (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci. Biotechnol. Biochem., 67, 225-243.
12. He,Z. et al. (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J., 1, 67-77.
13. He,Z. and Zhou,J. (2008) Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Appl. Environ. Microbiol., 74, 2957-2966.
14. He,Z.L. et al. (2008) Development and application of functional gene arrays for microbial community analysis. Trans. Nonferrous Met. Soc. China, 18, 1319-1327.
15. Held,G.A. (2006) Relationship between gene expression and observed intensities in DNA microarrays-a modeling study. Nucleic Acids Res., 34, e70.
16. Jaing,C. et al. (2008) A functional gene array for detection of bacterial virulence elements. PLoS ONE, 3, e2163.
17. Kane,M.D. et al. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res., 28, 4552-4557.
18. Kimes,N.E. et al. (2010) Microbial functional structure of "Montastraea faveolata", an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ. Microbiol., 12, 541-556.
19. Kottmann,R. et al. (2010) Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res., 38, D391-D395.
20. Leigh,M.B. et al. (2007) Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J., 1, 134-148.
21. Lemoine,S. et al. (2009) An evaluation of custom microarray applications: the oligonucleotide design challenge, Nucleic Acids Res., 37, 1726-1739.
22. Li,X. et al. (2005) Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res., 33, 6114-6123.
23. Liang,Y. et al. (2009) Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiol. Ecol., 70, 324-333.
24. Mason,O.U. et al. (2008) Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J., 3, 231-242.
25. Militon,C. et al. (2007) PhylArray: phylogenetic probe design algorithm for microarray. Bioinformatics, 23, 2550-2557.
26. Nordberg,E.K. (2005) YODA: selecting signature oligonucleotides. Bioinformatics, 21, 1365-1370.
27. Pozhitkov,A.E. et al. (2007) Oligonucleotide microarrays: widely applied poorly understood. Brief. Funct. Genomic Proteomic, 6, 141-148.
28. Rhee,S.-K. et al. (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol., 70, 4303-4317.
29. Thompson,J.D. et al. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
30. Van Nostrand,J.D. et al. (2009) GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ. Microbiol., 11, 2611-2626.
31. Vetriani,C., et al. (2003) Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the black sea. Appl. Environ. Microbiol., 69, 6481-6488.
32. Wang,F. et al. (2009) GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc. Natl Acad. Sci. USA, 106, 4840-4845.
33. Wang,X. and Seed,B. (2003) Selection of oligonucleotide probes for protein coding sequences. Bioinformatics, 19, 796-802.
34. 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.
35. Whitman,W.B. et al. (1998) Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA, 95, 6578-6583.
36. Wu,L. et al. (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl. Environ. Microbiol., 72, 4931-4941.
37. Yergeau,E. et al. (2007) Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J., 1, 163-179.