A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
<p>Abstract</p> <p>Background</p> <p>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 orga...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-04-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/185 |
| _version_ | 1828434314678763520 |
|---|---|
| author | Reifman Jaques Kumar Kamal Zavaljevski Nela Vijaya Satya Ravi |
| author_facet | Reifman Jaques Kumar Kamal Zavaljevski Nela Vijaya Satya Ravi |
| author_sort | Reifman Jaques |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Francisella tularensis </it>and <it>Yersinia pestis</it>, 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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-10T18:48:30Z |
| format | Article |
| id | doaj.art-9ad6788db037420299cc876fab343c4f |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T18:48:30Z |
| publishDate | 2008-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-9ad6788db037420299cc876fab343c4f2022-12-22T01:37:25ZengBMCBMC Bioinformatics1471-21052008-04-019118510.1186/1471-2105-9-185A high-throughput pipeline for designing microarray-based pathogen diagnostic assaysReifman JaquesKumar KamalZavaljevski NelaVijaya Satya Ravi<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Francisella tularensis </it>and <it>Yersinia pestis</it>, 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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/9/185 |
| spellingShingle | Reifman Jaques Kumar Kamal Zavaljevski Nela Vijaya Satya Ravi A high-throughput pipeline for designing microarray-based pathogen diagnostic assays BMC Bioinformatics |
| 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 |
| url | http://www.biomedcentral.com/1471-2105/9/185 |
| work_keys_str_mv | AT reifmanjaques ahighthroughputpipelinefordesigningmicroarraybasedpathogendiagnosticassays AT kumarkamal ahighthroughputpipelinefordesigningmicroarraybasedpathogendiagnosticassays AT zavaljevskinela ahighthroughputpipelinefordesigningmicroarraybasedpathogendiagnosticassays AT vijayasatyaravi ahighthroughputpipelinefordesigningmicroarraybasedpathogendiagnosticassays AT reifmanjaques highthroughputpipelinefordesigningmicroarraybasedpathogendiagnosticassays AT kumarkamal highthroughputpipelinefordesigningmicroarraybasedpathogendiagnosticassays AT zavaljevskinela highthroughputpipelinefordesigningmicroarraybasedpathogendiagnosticassays AT vijayasatyaravi highthroughputpipelinefordesigningmicroarraybasedpathogendiagnosticassays |