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Allermatchtm databases

Allermatchtm provides three databases of sequences of known allergenic proteins that have been listed by:
  1. the UniProt 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.

UniProt (previously referred to as UniProt)

The UniProt list of allergens refers to accessions on the UniProt 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 UniProt on December 4, 2007, contains 395 sequences with 316 unique allergen names. A number of sequenced in this database (72 sequences) do not occur in the Allermatchtm database of allergens listed by WHO-IUIS as of September 21, 2007. To view a list of all sequences of the UniProt allergen list within Allermatchtm, click here.

WHO-IUIS

The WHO-IUIS list contains allergens, for example maize allergen Zea m 14, each of which has been subdivided into one or more isoallergens. These isoallergens are allergenic proteins from the same source that show minor differences, such as single amino acid substitutions (for example, Zea m 14.0101 and Zea m 14.0102). 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 UniProt's, while considerable overlap exists between both lists. For a number of isoallergens, the WHO-IUIS refers to the same sequence database accession as UniProt, in which case the same sequence will be used for the both the allergen listed by WHO-IUIS and Uniprot. In addition, many (464) of the remaining allergens listed by WHO-IUIS but not by UniProt, the WHO-IUIS database provides sequences, which have consequently been used by Allermatch. For the 76 remaining allergens, references to sequence accessions stored in protein databases have been obtained from the WHO-IUIS list or from the following websites specialized in allergens:
  • Allergome (link)
  • FARRP - Food Allergy Research and Resource Program (link)
  • Biotechnology Information for Food Safety Database (link)
  • SDAP - Structural Database of Allergenic Proteins (link)
  • CSL - Central Science Laboratory, Allergen Database (link)
  • Informall (link)
Besides UniProt and WHO-IUIS, a small number (6) of sequences of allergens listed by WHO-IUIS and stored in the Allermatch tm database have been retrieved from two additional protein databases, EMBL (link) and PIR (link). The annotation of the sequences obtained from sources other than UniProt may not always provide details to the same level as in UniProt 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 UniProt 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 listed by WHO-IUIS on December 4, 2007, contains 863 sequences with 552 unique allergen names. For 40 allergens (corresponding to 47 isoallergens) listed by WHO-IUIS, no sequence accessions could be retrieved. To view a list of all sequences of the WHO-IUIS collection within Allermatchtm, click here..

Combination of UniProt 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 935 sequences with 588 unique allergen names. To see what is in this database click here..
Questions: Dr. Gijs Kleter
Updated: UniProt, December 4, 2007 (395 entries), WHO-IUIS December 21, 2007 (863 entries).