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SDAP - Structural Database of Allergenic Proteins
FAO/WHO Allergenicity Rules based on Sequence Homology
The FAO/WHO allergenicity rules
are presented in the Report of a Joint FAO/WHO Expert Consultation on Allergenicity of Foods Derived
from Biotechnology, 22-25 January 2001. As proposed in the
cross-reactivity between a query protein and a known allergen has to be considered when there is:
(a) more than 35% identity in the amino acid sequence of the expressed protein, using a window of 80 amino acids and a suitable gap penalty
(b) identity of 6 contiguous amino acids.
SDAP offers a flexible interface to check the FAO/WHO allergenicity rules against all allergens from the SDAP database. The user should follow the following steps:
1. Enter the name of the sequence
2. Paste or type your protein sequence as a string of single-letter amino acid codes
(lower-case amino acid codes will be translated into upper-case amino acid codes).
The maximum length of the sequence is 1000; sequences longer than 1000 amino acids will
be truncated after the first 1000 amino acids. Besides the codes of the 20 amino acids,
acceptable symbols are B (aspartate or asparagine), U (selenocysteine), and X (any
amino acid). The symbols Z, *, -, and . are translated into X (FASTA deletes these symbols
from its input). Any other input characters (including space and new line) will be deleted.
3. Perform a full FASTA alignment between the user sequence and all allergens from the SDAP database. Although this step is not part of the FAO/WHO allergenicity rules, it should be used to identify allergens that are highly similar with the query sequence. The user can change the maximum E score for the results of the full FASTA alignments.
4. Perform FASTA alignments for an 80 amino acids sliding window along the user sequence. The user can change the sequence identity cutoff from the value proposed by the FAO/WHO allergenicity rules (35%).
5. Perform an exact match search for contiguous amino acids. The FAO/WHO allergenicity rules recommend a number of six contiguous amino acids, but the user can change this value.
Search made with FASTA 3.45