Allermatchtm provides three databases of sequences of known allergenic proteins that have been listed by:
- the UniProt Protein Knowledgebase (link), and
- the list of allergen nomenclature of the joint World Health Organization and International Union of Immunological Societies (WHO-IUIS, link)
- A combination of these two databases.
UniProt (previously referred to as SwissProt)
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 July 11, 2012, contains 448 sequences with 374 unique allergen names. To view the list of all sequences of the UniProt allergen list within Allermatchtm, click here.
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 isoallergen listed by WHO-IUIS and the allergen listed by Uniprot. In addition, for many of the remaining allergens listed by WHO-IUIS but not by UniProt.s allergen list, WHO-IUIS provides references to accessions in the UniProt and GenBank/GenPept sequence databases, which have consequently been used by Allermatchtm.
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 Allermatchtm.
The Allermatchtm database of allergens listed by WHO-IUIS on August 12th, 2012, contains 1003 sequences with 985 unique isoallergen names. For 102 (iso)allergens listed by WHO-IUIS, no references to sequence database accessions were provided.
To view the 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 allergen list entries with the same UniProt accession only once. This database contains 1080 sequences with 692 unique allergen names. To see what is in this database click here.