AllFam
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Frequently asked questions
Frequently asked questions
AllFam construction and algorithms
- Which allergens are included in AllFam
- AllFam contains all allergens from the Allergome database
for which the protein sequence is deposited in the Uniprot database.
Since the introduction of the Allergenicity Scoring system in Allergome, the list of allergens in AllFam
is confined to proteins with experimentally confirmed allergenicity, i. e. binding of human IgE,
in vitro cell activation capability, positive skin tests or positive results of challenge tests.
These proteins are marked in the Allergome Allergenicity Scoring line (on top of the allergen monograph page)
by at least one green dot in the second group of scores. The Allergome Allergenicity Score is based on data
from the literature and continuously updated. In addition, allergens without specified route of exposure are
excluded from AllFam. This prevents IgE binding allergen homologues without allergological significance for
humans from being listed in AllFam (e.g. tropomyosins from sea spiders, yeast proteins used as controls in
laboratory tests).
- Why was Pfam selected as the protein family database AllFam is based on?
- Protein family definitions within Pfam are based on Hidden Markov Models (HMMs) that are
derived from manually compiled multiple sequence alignments. Hence the Pfam database combines
the reliability of manual editing with the sensitivity of profile HMMs. In addition, Pfam contains
more than 10,000 protein families and is therefore probably the most comprehensive protein family database.
- What is the difference between Pfam families and AllFam families
- For single-domain proteins, each Pfam family corresponds to an AllFam family. For multi-domain
proteins, Pfam domains are classified on the context they are found within:
(I) domains that occur only together with a single domain or set of domains (e. g. protease propeptides)
(II) domains that are found in combinations with different other domains (e. g. the hevein domain found
in class I chitinases, PR-4 proteins, and without a partner domain)
(III) domains that occur only together with a single domain or set of domains, but those partner domains
fall into category II (e. g. the barwin domain that is found together with the hevein domain)
For domains of categories II and III, corresponding AllFam families were created. Domains of category I
were merged with their partner domains into AllFam families that represent the whole multi-domain protein.
- How frequently is AllFam updated?
- AllFam is updated about once a month.
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AllFam user interface
- How can I find out which protein family my allergen belongs to?
- If the allergen of interest is already included in Allergome, you can search for the allergen
in the Allergome database, where you can find
links to AllFam allergen family fact sheets in the allergen monographs. If the allergen is not
included in Allegome or the link to AllFam is missing, go to the Pfam search page where
you can search for your protein by Uniprot accession number or compare your sequence to the Pfam database.
If you find a Pfam domain, you can search AllFam for allergen families
that contain this Pfam domain.
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Problems and errors
- Why are some allergens not listed in AllFam?
- This can have several reasons. First, AllFam lists only allergens with known sequences
or sequence fragments that are long enough to allow a classification into protein families.
Second, PfamA (the curated part of the Pfam database) currently covers only 74% of all sequences in Uniprot.
Thus, there are some allergens with known complete sequences that cannot be assigned to a protein
family (e. g. the latex allergen Hev b 5). Third, AllFam includes only allergens with experimentally
confirmed IgE binding capability or allergenic in vitro or in vivo activity. Thus some Allergome entries such as
Uniprot entries without associated published papers are not included in AllFam. Finally, the allergen may not
be included in Allergome. However, this is quite unlikely, because Allergome is continuously updated
with allergen data from several sources such as literature and sequence databases.
- An allergen is assigned the wrong protein family, who should I contact?
- Protein family assignment is based on sequence information obtained from Allergome. A wrong
classification may be caused by a wrong Uniprot accession number in Allergome. In this case,
contact the Allergome administrator for a correction.
In case of errors in the Allergen Family Fact Sheets in AllFam, please contact the
AllFam administrator.
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Miscellaneous
- How to cite AllFam
-
If you use data from AllFam in your work, please cite the following paper:
Radauer C, Bublin M, Wagner S, Mari A, Breiteneder H:
Allergens are distributed into few protein families and possess a restricted number of biochemical functions.
J Allergy Clin Immunol 2008, 121, 847-52.
[PubMed]
In addition, please include also the AllFam URL:
http://www.meduniwien.ac.at/allergens/allfam/.
- Contact
- Project leader, site administrator, database designer: Christian Radauer (christian.radauer@meduniwien.ac.at)
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