Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Terrat, Sébastien ^a,b   Peyretaillade, Eric ^a,b   Gonçalves, Olivier ^a,b   Dugat Bony, Eric ^a,b   Gravelat, Fabrice ^a,b   Moné, Anne ^a,b   Biderre Petit, Corinne ^a,b   Boucher, Delphine ^a,b   Troquet, Julien ^c   Peyret, Pierre ^a,b  

^a UNIVERSITÉ CLERMONT AUVERGNE   (France)

^b UNIVERSITÉ BLAISE PASCAL   (France)

^c NONE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIODEGRADATION KINETICS; GENERAL PUBLIC LICENSE; METABOLIC CAPACITIES; MICROBIAL COMMUNITIES; QUANTITATIVE REAL TIME PCR; SIMULTANEOUS ANALYSIS; SPHINGOMONAS PAUCIMOBILIS; USER FRIENDLY PROGRAM;

BIODEGRADATION; DESIGN; ENZYMES; EXPERIMENTS; GENE EXPRESSION; METABOLIC ENGINEERING; METABOLISM; MICROORGANISMS; ORGANIC POLLUTANTS; POLYCYCLIC AROMATIC HYDROCARBONS; POLYMERASE CHAIN REACTION; PROBES; SOIL POLLUTION; TOOLS;

MICROARRAYS;

SPHINGOMONAS PAUCIMOBILIS;

POLYCYCLIC AROMATIC HYDROCARBON; PRIMER DNA;

ALGORITHM; ARTICLE; BIOREMEDIATION; CHEMISTRY; COMPUTER PROGRAM; DNA MICROARRAY; DNA PROBE; GENETIC VARIABILITY; GENETICS; METABOLISM; METHODOLOGY; MICROARRAY ANALYSIS; MICROBIOLOGY; SOIL POLLUTANT; SPHINGOMONAS;

ALGORITHMS; BIODEGRADATION, ENVIRONMENTAL; DNA PRIMERS; DNA PROBES; GENETIC VARIATION; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYCYCLIC HYDROCARBONS, AROMATIC; SOFTWARE; SOIL MICROBIOLOGY; SOIL POLLUTANTS; SPHINGOMONAS;

EID: 77956873133     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-478     Document Type: Article

References (57)

1. Vieites JM, Guazzaroni M-E, Beloqui A, Golyshin PN, Ferrer M. Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 2009, 33(1):236-255. 10.1111/j.1574-6976.2008.00152.x, 19054115.
2. Schloss PD, Handelsman J. Toward a Census of Bacteria in Soil. PLoS Comput Biol 2006, 2(7):e92. 10.1371/journal.pcbi.0020092, 1513271,1513271, 16848637.
3. Torsvik V, Øvreås L. Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 2002, 5(3):240-245. 10.1016/S1369-5274(02)00324-7, 12057676.
4. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, et al. Functional metagenomic profiling of nine biomes. Nature 2008, 452(7187):629-632. 10.1038/nature06810, 18337718.
5. Urisman A, Fischer K, Chiu C, Kistler A, Beck S, Wang D, DeRisi J. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol 2005, 6(9):R78. 10.1186/gb-2005-6-9-r78, 1242213, 16168085.
6. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci USA 2002, 99(24):15687-15692. 10.1073/pnas.242579699, 137777, 12429852.
7. Warnecke F, Hess M. A perspective: Metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 2009, 142(1):91-95. 10.1016/j.jbiotec.2009.03.022, 19480952.
8. Artamonova I, Frishman G, Frishman D. Applying negative rule mining to improve genome annotation. BMC Bioinformatics 2007, 8(1):261. 10.1186/1471-2105-8-261, 1940032, 17659089.
9. Galperin MY, Koonin EV. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 2004, 32(18):5452-5463. 10.1093/nar/gkh885, 524295, 15479782.
10. Singh BK. Exploring microbial diversity for biotechnology: the way forward. Trends Biotechnol 2010, 28(3):111-116. 10.1016/j.tibtech.2009.11.006, 20005589.
11. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2001, 29(1):11-16. 10.1093/nar/29.1.11, 29800, 11125038.
12. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000, 28(1):45-48. 10.1093/nar/28.1.45, 102476, 10592178.
13. He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, et al. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 2007, 1(1):67-77. 10.1038/ismej.2007.2, 18043615.
14. Rhee S-K, Liu X, Wu L, Chong SC, Wan X, Zhou J. Detection of Genes Involved in Biodegradation and Biotransformation in Microbial Communities by Using 50-Mer Oligonucleotide Microarrays. Appl Environ Microbiol 2004, 70(7):4303-4317. 10.1128/AEM.70.7.4303-4317.2004, 444823, 15240314.
15. Wu L, Liu X, Schadt CW, Zhou J. Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification. Appl Environ Microbiol 2006, 72(7):4931-4941. 10.1128/AEM.02738-05, 1489353, 16820490.
16. Gao H, Yang ZK, Gentry TJ, Wu L, Schadt CW, Zhou J. Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification. Appl Environ Microbiol 2007, 73(2):563-571. 10.1128/AEM.01771-06, 1796964, 17098911.
17. Lemoine S, Combes F, Le Crom S. An evaluation of custom microarray applications: the oligonucleotide design challenge. Nucleic Acids Res 2009, 37(6):1726-1739. 10.1093/nar/gkp053, 2665234, 19208645.
18. Jabado OJ, Palacios G, Kapoor V, Hui J, Renwick N, Zhai J, Briese T, Lipkin WI. Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments. Nucleic Acids Res 2006, 34(22):6605-6611. 10.1093/nar/gkl966, 1747188, 17135211.
19. Wang X, Seed B. Selection of oligonucleotide probes for protein coding sequences. Bioinformatics 2003, 19(7):796-802. 10.1093/bioinformatics/btg086, 12724288.
20. Nordberg EK. YODA: selecting signature oligonucleotides. Bioinformatics 2005, 21(8):1365-1370. 10.1093/bioinformatics/bti182, 15572465.
21. Pozhitkov AE, Tautz D, Noble PA. Oligonucleotide microarrays: widely applied poorly understood. Brief Funct Genomics 2007, 6(2):141-148.
22. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ. Assessment of the sensitivity and specificity of oligonucleotide (50 mer) microarrays. Nucleic Acids Res 2000, 28(22):4552-4557. 10.1093/nar/28.22.4552, 113865, 11071945.
23. Missaoui M, Hill D, Peyret P. A comparison of algorithms for a complete backtranslation of oligopeptides. Int J Comput Biol Drug Des 2008, 1(1):26-38. 10.1504/IJCBDD.2008.018708, 20054999.
24. Keck A, Conradt D, Mahler A, Stolz A, Mattes R, Klein J. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 2006, 152(7):1929-1940. 10.1099/mic.0.28783-0, 16804169.
25. Ní Chadhain S, Moritz E, Kim E, Zylstra G. Identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from Sphingobium yanoikuyae B1. J Ind Microbiol Biotechnol 2007, 34(9):605-613. 10.1007/s10295-007-0235-3, 17647036.
26. Pinyakong O, Habe H, Yoshida T, Nojiri H, Omori T. Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2. Biochem Biophys Res Commun 2003, 301(2):350-357. 10.1016/S0006-291X(02)03036-X, 12565867.
27. Romine MF, Stillwell LC, Wong K-K, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD. Complete Sequence of a 184-Kilobase Catabolic Plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 1999, 181(5):1585-1602. 93550, 10049392.
28. Demaneche S, Meyer C, Micoud J, Louwagie M, Willison JC, Jouanneau Y. Identification and Functional Analysis of Two Aromatic-Ring-Hydroxylating Dioxygenases from a Sphingomonas Strain That Degrades Various Polycyclic Aromatic Hydrocarbons. Appl Environ Microbiol 2004, 70(11):6714-6725. 10.1128/AEM.70.11.6714-6725.2004, 525238, 15528538.
29. Rimour S, Hill D, Militon C, Peyret P. GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics 2005, 21(7):1094-1103. 10.1093/bioinformatics/bti112, 15531611.
30. Mueller J, Chapman P, Blattmann B, Pritchard P. Isolation and characterization of a fluoranthene-utilizing strain of Pseudomonas paucimobilis. Appl Environ Microbiol 1990, 56(4):1079-1086. 184346, 2339870.
31. Story SP, Parker SH, Kline JD, Tzeng TR, Mueller JG, Kline EL. Identification of four structural genes and two putative promoters necessary for utilization of naphthalene, phenanthrene, fluoranthene by Sphingomonas paucimobilis var. EPA505. Gene 2000, 260(1-2):155-169. 10.1016/S0378-1119(00)90445-1, 11137301.
32. Cho O, Choi KY, Zylstra GJ, Kim YS, Kim SK, Lee JH, Sohn HY, Kwon GS, Kim YM, Kim E. Catabolic role of a three-component salicylate oxygenase from Sphingomonas yanoikuyae B1 in polycyclic aromatic hydrocarbon degradation. Biochem Biophys Res Commun 2005, 327(3):656-662. 10.1016/j.bbrc.2004.12.060, 15649397.
33. Pinyakong O, Habe H, Supaka N, Pinpanichkarn P, Juntongjin K, Yoshida T, Furihata K, Nojiri H, Yamane H, Omori T. Identification of novel metabolites in the degradation of phenanthrene by Sphingomonas sp. strain P2. FEMS Microbiol Lett 2000, 191(1):115-121. 10.1111/j.1574-6968.2000.tb09327.x, 11004408.
34. Jakoncic J, Jouanneau Y, Meyer C, Stojanoff V. The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. FEBS J 2007, 274(10):2470-2481. 10.1111/j.1742-4658.2007.05783.x, 17451434.
35. Pinyakong O, Habe H, Omori T. The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J Gen Appl Microbiol 2003, 49(1):1-19. 10.2323/jgam.49.1, 12682862.
36. Keseler IM, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, et al. EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res 2009, 37(suppl_1):D464-470. 10.1093/nar/gkn751, 2686493, 18974181.
37. Adler P, Reimand J, Janes J, Kolde R, Peterson H, Vilo J. KEGGanim: pathway animations for high-throughput data. Bioinformatics 2008, 24(4):588-590. 10.1093/bioinformatics/btm581, 18056068.
38. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36(suppl_1):D480-484. 2238879, 18077471.
39. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2010, 38(suppl_1):D473-479. 10.1093/nar/gkp875, 2808959, 19850718.
40. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 2004, 32(suppl_1):D431-433. 10.1093/nar/gkh081, 308815, 14681450.
41. Corpet F, Gouzy J, Kahn D. The ProDom database of protein domain families. Nucleic Acids Res 1998, 26(1):323-326. 10.1093/nar/26.1.323, 147246, 9399865.
42. Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34(suppl_1):D363-368. 10.1093/nar/gkj123, 1347485, 16381887.
43. Fulton D, Li Y, Laird M, Horsman B, Roche F, Brinkman F. Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics 2006, 7(1):270. 10.1186/1471-2105-7-270, 1524997, 16729895.
44. Eklund AC, Friis P, Wernersson R, Szallasi Z. Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization. Nucleic Acids Research 2009, 38(4):e27. 10.1093/nar/gkp1116, 2831327, 19969549.
45. Mueckstein U, Leparc G, Posekany A, Hofacker I, Kreil D. Hybridization thermodynamics of NimbleGen Microarrays. BMC Bioinformatics 2010, 11(1):35. 10.1186/1471-2105-11-35, 2823707, 20085625.
46. Royce TE, Rozowsky JS, Gerstein MB. Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res 2007, 35(15):e99. 10.1093/nar/gkm549, 1976448, 17686789.
47. Liang Y, Li G, Van Nostrand JD, He Z, Wu L, Deng Y, Zhang X, Zhou J. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiol Ecol 2009, 70(2):324-333.
48. Liang Y, Nostrand JDV, Wang J, Zhang X, Zhou J, Li G. Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil. Chemosphere 2009, 75(2):193-199. 10.1016/j.chemosphere.2008.12.007, 19144375.
49. Bau S, Schracke N, Kränzle M, Wu H, Stähler P, Hoheisel J, Beier M, Summerer D. Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays. Anal Bioanal Chem 2009, 393(1):171-175. 10.1007/s00216-008-2460-7, 18958448.
50. Summerer D, Wu H, Haase B, Cheng Y, Schracke N, Stähler CF, Chee MS, Stähler PF, Beier M. Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing. Genome Res 2009, 19(9):1616-1621. 10.1101/gr.091942.109, 2752126, 19638418.
51. Zhou J, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol 1996, 62(2):316-322. 167800, 8593035.
52. Verdick D, Handran S, Pickett S. Key considerations for accurate microarray scanning and image analysis. DNA array image analysis: nuts and bolts 2002, 83-98. LLC DP: Salem, MA, Kamberova G.
53. Wang X, He H, Li L, Chen R, Deng XW, Li S. NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics 2006, 22(23):2955-2957. 10.1093/bioinformatics/btl525, 17038341.
54. He Z, Zhou J. Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis. Appl Environ Microbiol 2008, 74(10):2957-2966. 10.1128/AEM.02536-07, 2394959, 18344333.
55. Sambrook J, Fritsch E, Maniatis T. Molecular cloning: A Laboratory Manual - Third Edition. 2001, Cold Spring Laboratory Harbor Press, U.S.A.
56. Staden R. The staden sequence analysis package. Mol Biotechnol 1996, 5(3):233-241. 10.1007/BF02900361, 8837029.
57. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.