Skip Navigation

Nucleic Acids Research 2006 34(13):3779-3793; doi:10.1093/nar/gkl467
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (724K) Freely available
Right arrow Screen PDF (724K) Freely available
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 ISI Web of Science
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (5)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Soeria-Atmadja, D.
Right arrow Articles by Hammerling, U.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Soeria-Atmadja, D.
Right arrow Articles by Hammerling, U.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 23 August 2006

Nucleic Acids Research, 2006, Vol. 34, No. 13 3779-3793
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article

Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning

D. Soeria-Atmadja, T. Lundell, M. G. Gustafsson1,2,* and U. Hammerling*

Division of Toxicology, National Food Administration PO Box 622, SE-751 26 Uppsala, Sweden 1 Department of Engineering Sciences, Uppsala University PO Box 534, SE-751 21 Uppsala, Sweden 2 Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory SE-751 85 Uppsala, Sweden

*To whom correspondence should be addressed. Email: ulfh{at}slv.se

*Correspondence may also be addressed to M. G. Gustafsson. Tel: +46 18 4713229; Fax: +46 18 555096; Email: mg{at}angstrom.uu.se Present address: M. G. Gustafsson, Department of Medical Sciences, Uppsala University, Uppsala University Hospital, SE-751 85 Uppsala, Sweden

Received April 4, 2006. Revised June 20, 2006. Accepted June 20, 2006.

The placing of novel or new-in-the-context proteins on the market, appearing in genetically modified foods, certain bio-pharmaceuticals and some household products leads to human exposure to proteins that may elicit allergic responses. Accurate methods to detect allergens are therefore necessary to ensure consumer/patient safety. We demonstrate that it is possible to reach a new level of accuracy in computational detection of allergenic proteins by presenting a novel detector, Detection based on Filtered Length-adjusted Allergen Peptides (DFLAP). The DFLAP algorithm extracts variable length allergen sequence fragments and employs modern machine learning techniques in the form of a support vector machine. In particular, this new detector shows hitherto unmatched specificity when challenged to the Swiss-Prot repository without appreciable loss of sensitivity. DFLAP is also the first reported detector that successfully discriminates between allergens and non-allergens occurring in protein families known to hold both categories. Allergenicity assessment for specific protein sequences of interest using DFLAP is possible via ulfh{at}slv.se.


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
 Nucleic Acids ResHome page
A. M. Barrio, D. Soeria-Atmadja, A. Nister, M. G. Gustafsson, U. Hammerling, and E. Bongcam-Rudloff
EVALLER: a web server for in silico assessment of potential protein allergenicity
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W694 - W700.
[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.