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OFRG

Brief Introduction

The oligonucleotide fingerprinting of ribosomal RNA genes(OFRG) is a method that permits the identification of arrayed ribosomal RNA genes (rDNA) through a series of hybridizaition experiments using small DNA probes. This approach involves new array-based methods and innovative data analysis strategies developed by our research group. It provides a cost effective means to extensively analyze microbial communities and should have application in medicine, biotechnology and ecosystem studies. Utilization of this new experimental approach has and will continue to lead to a greater understanding of the organisms inhabiting our planet, their functional roles in ecosystems and their potential for biotechnology. This project is funded by NSF DBI Award #0133265. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.


Personnel

James Borneman  Profesor of Plant Pathology Marek Chrobak  Professor of Computer Science
David Crowley  Associate Professor of Environmental Sciences Daniel Jeske  Professor of Statistics
Tao Jiang  Professor of Computer Science Jingxiao Ye  Graduate Student in Plant Pathology
Yu-Ting Huang  Graduate Student in Computer Science


Alumni

Elizabeth Bent  Postdoctoral Researcher in Plant Pathology Gianluca Della Vedova  
Andres Figueroa  Ph.D. in Computer Science Qi Fu  Ph.D. in Computer Science
Katechan Jampachaisri  Graduate Student in Statistics Zheng Liu  Ph.D. in Computer Science
Jim Press  Distinguished Professor of Statistics Lea Valinsky   Postdoctoral Researcher in Plant Pathology


Tools and Server

rDNA Sequence Retrieval

The tool of rDNA sequence retrieval is developed for sequence acquisition and database construction. Given primers for a taxa, rRNA genes in the taxa will be downloaded from GenBank and edited by approximate string matching and homology searching algorithms. The sequences will be used by the program OFRG ProbeTools to design optimized probe sets for a specific target microbial community.

 

ProbeTools

A probe set design package. This is a software package for designing oligonucleotide probes for OFRG hybridization experiments. The general goal is to design a small collection of probes that will collectively discriminate all, or almost all, clones within a specified population. The algorithm follows an interactive process involving successive rounds of both theoretical design and experimental validation to provide probes that hybridize in the predicted manner. The qualified probe sets are used to hybridize clone samples for the analysis of various groups of microorganisms.

 

OFRG Central

This is the database where all information concerning an OFRG project is stored, including information about the project, environment, sample, extraction methods, clone libraries, control clones, probe sets, hybridization results, microarray images, binarized fingerprints, cluster analysis results, etc. The database allows users to reuse data from previous work in new experiments, and it includes tools for producing various reports. Not only does the database help the experimentalists involved in the project to manage their data, it also facilitates subsequent data analyses by using the tools provided.


Downloadable Software

Macros

Various excel macros are designed to facilitate raw data analysis. They can be used to extract signals from microarray images, binarize intensity values, and generate theoretical fingerprints.

 

GCPAT

Greedy Clique Partition pAckage Tool (GCPAT) is developed to visulize and analyze hybridization experiments of a set of ribosomal gene clones. It integrates various tools for OFRG data analysis such as clone identification, clustering and visulization.

 

CloneTools

CloneTools package is comprised of several tools: (1) Control clone picker; (2) FASTA generator; (3) Conserved region finder; (4) Sequence filter; (5) Clone plate reorder; (6) Synthetic fingerprint generator.

 

PRISE2

PRImer Selector 2(PRISE2) is an interactive software package for PCR primer design. PRISE2 enables the design of sequence-specific / sequence-selective PCR primers/probes. One important feature of PRISE2 is that it automates the task of placing primer-template mismatches at the 3' end of the primers and the middle of the probes - a property that is crucial for sequence selectivity / specificity. PRISE2 was designed and developed by researchers and graduate students involved in the OFRG project. We stress, however, that PRISE2 is a generally applicable primer-design tool, not specific to its application in OFRG.


Publications

Book Chapters

1. Valinsky L., Scupham A., Vedova G.D., Liu Z., Figueroa A., Jampachaisri K., Yin B., Bent E., Mancini-Jones, R., Press J., Jiang T., and Borneman J. 2004 Oligonucleotide Fingerprinting of Ribosomal RNA Genes (OFRG), p. 569-585. In G. A. Kowalchuk, F. J. de Bruijn, I. M. Head, A. D. L. Akkermans, J. D.van Elsas (ed.) Molecular Microbial Ecology Manual (2nd ed). Kluwer Academic Publishers, Dordrecht, The Netherlands.
2. Borneman J., J.O. Becker, E. Bent, B. Lanoil, B. McSpadden Gardener, R. Olatinwo, L. Presley, A.J. Scupham, L. Valinsky, B. Yin. Identifying microorganisms involved in specific in situ functions: experimental design considerations for rRNA gene-based population studies and sequence-selective PCR assays, In Christon Hurst (ed.) Manual for Environmental Microbiology (3rd ed). ASM Press (in press).

Papers

1. Q. Fu, P. Ruegger, E. Bent, M. Chrobak, J. Borneman. PRISE (PRImer SElector): Software for designing sequence-selective PCR primers. Journal of Microbiological Methods (2008) 72(3):263-267.
2. Q. Fu, E. Bent, J. Borneman, M. Chrobak, N. E. Young. Algorithmic approaches to selecting control clones in DNA array hybridization experiments. Journal of Bioinformatics and Computational Biology (2007) 5(4):937-961.
3. D. R. Jeske, Z. Liu, E. Bent, J. Borneman. Classification rules that Include neutral zones and their application to microbial community pofiling. Communications in Statistics - Theory and Methods (2007) 36:1965-1980.
4. E. Bent, B. Yin, A. Figueroa, J. Ye, Q. Fu, Z. Liu, V. McDonald, D. Jeske, T. Jiang, J. Borneman. Development of a 9,600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot. Journal of Microbiological Methods (2006) 67(1):171-180.
5. Alexandra J Scupham, Laura L. Presley, Bo Wei, Elizabeth Bent, Natasha Griffith, Michael McPherson, Feilin Zhu, Oluwadayo Oluwadara, Nagesh Rao, Jonathan Braun, and James Borneman. Abundant and diverse fungal microbiota in the murine intestine. Applied and Environmental Microbiology (2006) 72:793-801.
6. Z. Liu, J. Borneman, T. Jiang. A software system for gene sequence database construction based on fast approximate string matching. International Journal of Bioinformatics Research and Applications (2006) 1:273-291.
7. Q. Fu, J. Borneman, J. Ye, M. Chrobak. Improved probe selection for DNA arrays using nonparametric kernel density estimation. Proceedings of the 27th Annual International Conference of the IEEE EMBS (2005) 902-905.
8. Z. Liu, X. Chen, J. Borneman, T. Jiang. A fast algorithm for approximate string matching on gene sequences. Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (2005) LNCS 3537, p. 79-90.
9. K. Jampachaisri, L. Valinsky, J. Borneman, S. J. Press. Classification of oligonucleotide fingerprints: Application for Microbial Community and Gene Expression Analyses. Bioinformatics (2005) 21:3122-3130.
10. Tiffany Huang, Bo Wei, Peter Velazquez, James Borneman and Jonathan Braun. Commensal microbiota alter the abundance and TCR responsiveness of splenic naive CD4+ T lymphocytes. Clinical Immunology (2005) 117:221-230.
11. A. Figueroa, J. Borneman, and T. Jiang. Clustering binary fingerprint vectors with missing values for DNA array data analysis. Journal of Computational Biology (2004) 11(5):887-901.
12. A. Figueroa, Z. Liu, R. Mancini-Jones, J. Borneman, T. Jiang: Building phylogenetic trees from binary oligonucleotide fingerprint vectors. Proceedings of the 26th Annual International Conferences of the IEEE EMBS (2004) 2844-2847.
13. Z. Liu, J. Borneman, T. Jiang: A software system for gene sequence database construction. Proceedings of the 26th Annual International Conferences of the IEEE EMBS (2004) 2797-2800.
14. J. Borneman, R. Olatinwo, B. Yin and J. O. Becker: An experimental approach for identifying microorganisms involved in specified functions: utilisation for understanding a nematode suppressive soil. Australasian Plant Pathology (2004) 33(2):151-155.
15. B. Yin, L. Valinsky, X. Gao, J.O. Becker, and J. Borneman: Identification of fungal rDNA associated with soil suppressiveness against Heterodera schachtii using oligonucleotide fingerprinting of ribosomal RNA genes. Phytopathology (2003) 93:1006-1013.
16. B. Yin, L. Valinsky, X. Gao, J.O. Becker, and J. Borneman: Bacterial rDNA associated with soil suppressiveness against the plant-parasitic nematode Heterodera schachtii. Applied and Environmental Microbiology (2003) 69:1573-1580.
17. A. Figueroa, J. Borneman, and T. Jiang.: Clustering binary fingerprint vectors with missing values for DNA array data analysis. Proc. of 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference (CSB) (2003) 38-47.
18. L. Valinsky, G. Della Vedova, A. Scupham, S. Alvey, A. Figueroa, B. Yin, R. Hartin, M. Chrobak, D. Crowley, T. Jiang, and J. Borneman.: Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Applied and Environmental Microbiology (2002) 68(7):3243-3250.
19. L. Valinsky, G. Della Vedova, T. Jiang, and J. Borneman: Oligonucleotide fingerprinting of ribosomal RNA genes for analysis of fungal community composition. Applied and Environmental Microbiology (2002) 12:5999-6004.
20. J. Borneman, M. Chrobak, G.D. Vedova, A. Figueroa, and T. Jiang: Probe Selection algorithms with applications in the analysis of microbial communities. Bioinformatics (2001) 17, S39-S48.
21. Y.T. Huang, J.I. Yang, M. Chrobak, J. Borneman.: PRISE2: Software for Designing Sequence-Selective PCR Primers and Probes. Manuscript under submission.

Posters

1. E. Bent, R. Fischer, J.O. Becker and J. Borneman. 2004. Quantitative and qualitative differences in bacterial and fungal DNA extracted from California soils using three common DNA extraction methods. 10th International Symposium on Microbial Ecology (Cancun, Mexico) August 23-27 2004.
2. R. Olatinwo, B. Yin, J.O.Becker, E. Bent and J. Borneman. 2004. A three-phased approach for identifying microorganisms involved in specific functions: identification of microorganisms in a nematode-suppressive soil. 10th International Symposium on Microbial Ecology (Cancun, Mexico) August 23-27 2004.
3. E. Bent, R. Fischer, J.O. Becker and J. Borneman. 2004. Quantitative and qualitative differences in bacterial DNA extracted from California soils using three common DNA extraction methods. Abstract A02, Detailed MethodsResultsPoster Canadian Society of Microbiologists 54th Annual Meeting (Edmonton AB) June 20-23, 2004.
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Copyright @ by Oligonucleotide Fingerprinting of Ribosomal RNA Genes(OFRG) Group (zliu@cs.ucr.edu, qfu@cs.ucr.edu), 2002

Last Modified on 04/25/2013