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A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
BACKGROUND: We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375140/ https://www.ncbi.nlm.nih.gov/pubmed/18402679 http://dx.doi.org/10.1186/1471-2105-9-185 |
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author | Vijaya Satya, Ravi Zavaljevski, Nela Kumar, Kamal Reifman, Jaques |
author_facet | Vijaya Satya, Ravi Zavaljevski, Nela Kumar, Kamal Reifman, Jaques |
author_sort | Vijaya Satya, Ravi |
collection | PubMed |
description | BACKGROUND: We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design process is implemented in a high-performance computing software pipeline that incorporates major algorithmic improvements over a previous version to both reduce computation time and improve specificity assessment. RESULTS: The algorithmic improvements result in significant reduction in runtimes, with the updated pipeline being nearly up to five-times faster than the previous version. The improvements in specificity assessment, based on multiple specificity criteria, result in robust and consistent evaluation of cross-hybridization with nontarget sequences. In addition, the multiple criteria provide finer control on the number of resulting fingerprints, which helps in obtaining a larger number of fingerprints with high specificity. Simulation tests for Francisella tularensis and Yersinia pestis, using a well-established hybridization model to estimate cross-hybridization with nontarget sequences, show that the improved specificity criteria yield a larger number of fingerprints as compared to using a single specificity criterion. CONCLUSION: The faster runtimes, achieved as the result of algorithmic improvements, are critical for extending the pipeline to process multiple target genomes. The larger numbers of identified fingerprints, obtained by considering broader specificity criteria, are essential for designing probes for hard-to-distinguish target sequences. |
format | Text |
id | pubmed-2375140 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-23751402008-05-09 A high-throughput pipeline for designing microarray-based pathogen diagnostic assays Vijaya Satya, Ravi Zavaljevski, Nela Kumar, Kamal Reifman, Jaques BMC Bioinformatics Methodology Article BACKGROUND: We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design process is implemented in a high-performance computing software pipeline that incorporates major algorithmic improvements over a previous version to both reduce computation time and improve specificity assessment. RESULTS: The algorithmic improvements result in significant reduction in runtimes, with the updated pipeline being nearly up to five-times faster than the previous version. The improvements in specificity assessment, based on multiple specificity criteria, result in robust and consistent evaluation of cross-hybridization with nontarget sequences. In addition, the multiple criteria provide finer control on the number of resulting fingerprints, which helps in obtaining a larger number of fingerprints with high specificity. Simulation tests for Francisella tularensis and Yersinia pestis, using a well-established hybridization model to estimate cross-hybridization with nontarget sequences, show that the improved specificity criteria yield a larger number of fingerprints as compared to using a single specificity criterion. CONCLUSION: The faster runtimes, achieved as the result of algorithmic improvements, are critical for extending the pipeline to process multiple target genomes. The larger numbers of identified fingerprints, obtained by considering broader specificity criteria, are essential for designing probes for hard-to-distinguish target sequences. BioMed Central 2008-04-10 /pmc/articles/PMC2375140/ /pubmed/18402679 http://dx.doi.org/10.1186/1471-2105-9-185 Text en Copyright © 2008 Satya et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Vijaya Satya, Ravi Zavaljevski, Nela Kumar, Kamal Reifman, Jaques A high-throughput pipeline for designing microarray-based pathogen diagnostic assays |
title | A high-throughput pipeline for designing microarray-based pathogen diagnostic assays |
title_full | A high-throughput pipeline for designing microarray-based pathogen diagnostic assays |
title_fullStr | A high-throughput pipeline for designing microarray-based pathogen diagnostic assays |
title_full_unstemmed | A high-throughput pipeline for designing microarray-based pathogen diagnostic assays |
title_short | A high-throughput pipeline for designing microarray-based pathogen diagnostic assays |
title_sort | high-throughput pipeline for designing microarray-based pathogen diagnostic assays |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375140/ https://www.ncbi.nlm.nih.gov/pubmed/18402679 http://dx.doi.org/10.1186/1471-2105-9-185 |
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