Skip Navigation



Nucleic Acids Research Advance Access published online on September 29, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl565
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1136K) Freely available
Right arrow Screen PDF (1137K) Freely available
Right arrow Supplementary Material
Right arrow All Versions of this Article:
34/18/5300    most recent
gkl565v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Malanoski, A. P.
Right arrow Articles by Stenger, D. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Malanoski, A. P.
Right arrow Articles by Stenger, D. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published by Oxford University Press 2006

Computational Biology

Automated identification of multiple micro-organisms from resequencing DNA microarrays

Anthony P. Malanoski*, Baochuan Lin, Zheng Wang, Joel M. Schnur and David A. Stenger

Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory Washington DC 20375, USA

*To whom correspondence should be addressed. Tel: +1 202 404 5432; Fax: +1 202 767 9594; Email: anthony.malanoski{at}nrl.navy.mil

Received May 9, 2006. Revised July 18, 2006. Accepted July 19, 2006.

There is an increasing recognition that detailed nucleic acid sequence information will be useful and even required in the diagnosis, treatment and surveillance of many significant pathogens. Because generating detailed information about pathogens leads to significantly larger amounts of data, it is necessary to develop automated analysis methods to reduce analysis time and to standardize identification criteria. This is especially important for multiple pathogen assays designed to reduce assay time and costs. In this paper, we present a successful algorithm for detecting pathogens and reporting the maximum level of detail possible using multi-pathogen resequencing microarrays. The algorithm filters the sequence of base calls from the microarray and finds entries in genetic databases that most closely match. Taxonomic databases are then used to relate these entries to each other so that the microorganism can be identified. Although developed using a resequencing microarray, the approach is applicable to any assay method that produces base call sequence information. The success and continued development of this approach means that a non-expert can now perform unassisted analysis of the results obtained from partial sequence data.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Clin. Microbiol. Rev.Home page
M. B. Miller and Y.-W. Tang
Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology
Clin. Microbiol. Rev., October 1, 2009; 22(4): 611 - 633.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
B. Lin, A. P. Malanoski, Z. Wang, K. M. Blaney, N. C. Long, C. E. Meador, D. Metzgar, C. A. Myers, S. L. Yingst, M. R. Monteville, et al.
Universal Detection and Identification of Avian Influenza Virus by Use of Resequencing Microarrays
J. Clin. Microbiol., April 1, 2009; 47(4): 988 - 993.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. P. Malanoski, B. Lin, and D. A. Stenger
A model of base-call resolution on broad-spectrum pathogen detection resequencing DNA microarrays
Nucleic Acids Res., June 1, 2008; 36(10): 3194 - 3201.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
B. Lin, K. M. Blaney, A. P. Malanoski, A. G. Ligler, J. M. Schnur, D. Metzgar, K. L. Russell, and D. A. Stenger
Using a Resequencing Microarray as a Multiple Respiratory Pathogen Detection Assay
J. Clin. Microbiol., February 1, 2007; 45(2): 443 - 452.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.