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Allermatchtm databases

Allermatchtm provides three databases of sequences of known allergenic proteins that have been listed by:
  1. the SwissProt/TrEMBL Protein Knowledgebase (link), and
  2. the list of allergen nomenclature of the joint World Health Organization and International Union of Immunological Societies (WHO-IUIS, link)
  3. A combination of these two databases.

SwissProt

The SwissProt list of allergens refers to accessions on the SwissProt website, which contain well-annotated sequences, among others with information on the location of signal- and pro-peptides within sequences. In case signal- and pro-peptides are indicated, they are removed from the allergen sequences prior to addition of the sequences to the Allermatchtm database. This processing of sequences is in compliance with the recommendations of the FAO/WHO Expert Consultation on the evaluation of potential allergenicity of genetically modified foods (2001; link) in preparation of the Codex alimentarius' guidelines for the safety assessment of foods derived through biotechnology.

The Allermatchtm database of allergens listed by SwissProt on December 20, 2004, contains 368 sequences. A number of sequences of this database (111 sequences) do not occur in the Allermatchtm database of allergens and isoallergens listed by WHO-IUIS as of September 12, 2005. To view a list of all sequences of the Swissprot allergen list within Allermatchtm, click here.

WHO-IUIS

The WHO-IUIS list contains two sections, one section for allergens and the other for isoallergens, i.e. allergenic proteins from the same source that show minor differences, such as single amino acid substitutions. This list contains allergenic proteins that have been registered following submission, for example by scientists who have discovered a new allergen. For registration, the allergenic protein should comply with certain requirements, such as a minimal number of patients that have shown reactivity towards this protein, as well as a minimal prevalence (5 percent) of reactivity among these patients. The WHO-IUIS list is more extensive than that of SwissProt's, while considerable overlap exists between both lists. For a number of allergens and isoallergens, the WHO-IUIS does not provide references to sequence accessions in protein databases. In such cases, information on accessions, if available, is retrieved from the following websites specialized in allergens:
  • FARRP - Food Allergy Research and Resource Program (link)
  • Biotechnology Information for Food Safety Database (link)
  • SDAP - Structural Database of Allergenic Proteins (link)
  • Allergome (link)
  • CSL - Central Science Laboratory, Allergen Database (link)
  • Informall (link)
Besides SwissProt, a number of sequences of allergens and isoallergens listed by WHO-IUIS and stored in the Allermatch tm database have been retrieved from two additional protein databases, GenPept (link) and PIR (link). The annotation of these sequences may not always provide details to the same level as in SwissProt accessions, such as signal- and pro-peptides not being indicated. When the occurrence of signal- and pro-peptides is indicated by the accessions, these peptides are removed from the sequences prior to storage in Allermatch tm.

Compared to the SwissProt list, the use of the more extensive sequence database based on the WHO-IUIS list reduces the risk of missing an allergen (false negative), while, on the other hand, it also increases the risk of identifying false positives due to varying accuracy of the sequence annotations.

The Allermatchtm database of allergens and isoallergens listed by WHO-IUIS on September 12, 2005, contains 681 sequences, including 430 and 251 sequences of allergens and isoallergens, respectively. For 64 allergens and 22 isoallergens listed by WHO-IUIS, no sequence accessions could be retrieved. Two sequences, allergens Equ c 2 (2 sequences) occur in both the allergen and isoallergen sections of the WHO-IUIS database of Allermatchtm. To view a list of all sequences of the WHO-IUIS collection within Allermatchtm, click here..

Combination of SwissProt and WHO-IUIS

This database contains a non redundant combination of the two other databases. Redundancy has been removed by including those sequences with the same allergen name only once. This database contains 792 sequences. To see what is in this database click here..
Questions: Dr. Gijs Kleter
Updated: SwissProt, December 20 2005 (368 entries), WHO-IUIS September 12, 2005 (681 entries).