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Bioinformatics Advance Access originally published online on February 11, 2009
Bioinformatics 2009 25(7):979-980; doi:10.1093/bioinformatics/btp077
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© 2009 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-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information

Joo Chuan Tong 1, Shen Jean Lim 2, Hon Cheng Muh 3, Fook Tim Chew 3 and Martti T. Tammi 2,3,*

1Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis, South Tower, Singapore 138632, 2Department of Biochemistry, Yong Loo Lin School of Medicine and 3Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543

*To whom correspondence should be addressed.


  Abstract

Summary: A variety of specialist databases have been developed to facilitate the study of allergens. However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases. Each entry was manually verified, classified and hyperlinked to major databases including Swiss-Prot, Protein Data Bank (PDB), Gene Ontology (GO), Pfam and PubMed. The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission. The latest version contains information of 1593 allergen sequences (496 IUIS allergens, 978 experimentally verified allergens and 119 new sequences), 56 IgE epitope sequences, 679 links to PDB structures and 155 links to Pfam domains.

Availability: Allergen Atlas is freely available at http://tiger.dbs.nus.edu.sg/ATLAS/.

Contact: martti{at}nus.edu.sg.

Associate Editor: Dmitrij Frishman

Received on November 21, 2008; revised on February 5, 2009; accepted on February 5, 2009

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