Information Technology Reference
In-Depth Information
5.2.3.3 SDAP
SDAP (Structural Database of Allergenic Proteins) is a specialized allergen database
that incorporates information obtained from the IUIS list of allergens, Swiss-Prot,
PIR (Protein Information Resource), GenBank, GenPept, and the literature. However,
the entries in SDAP are guided by the IUIS list of allergens and isoallergens. SDAP
which has been static since January 2005 contains 737 allergens and isoallergens,
829 protein sequences, and 22 IgE and IgG epitopes.
Each record in SDAP contains the name of the allergen, the species that the
allergen originates from, protein sequences, nucleotide sequences, Pfam (Bateman,
Coin, Durbin, Finn, Hollich, Griffiths-Jones, Khanna, Marshall, Moxon, Sonnhammer,
Studholme, Yeats, and Eddy 2004), protein domains, 3D protein structure, and IgE
epitopes. The IgE epitope information was extracted from the literature. The epitope
information makes SDAP rather unique and useful, as it is one of the few databases
that contain this information. Records in SDAP can be searched by their names, the
allergen source, the description, and the allergen type. In addition to the search
facilities, there are compilations of allergens according to alphabetical order, allergens
containing PDB structures, allergens containing 3D models, allergens containing
epitopes, and various classes of allergens.
Other than containing a comprehensive set of allergen data, SDAP includes
computational tools for FASTA (Pearson 1994), sequence similarity search, allergen
analysis, and allergenicity prediction. The FAO/WHO allergenicity test evaluates the
allergenicity of a given protein sequence against the dataset present in SDAP. In
addition, SDAP includes two unique data searching tools. The first is an exact
matching tool for searching a query protein sequence against SDAP. This method is
useful if the query protein sequence is an epitope sequence. Any SDAP allergens
having the same subsequence as the query epitope sequence will be retrieved. The
result may then be used as evidence for cross-reactivity between the query sequence
and the matched SDAP allergen. If the SDAP allergen has a defined epitope, the
search result also provides a link to it.
However, the exact matching method is limited to detecting allergens with
identical epitopes. This is hardly practical as the same IgE molecule may bind to two
similar but not identical epitopes as seen in cross-reactivity. The second method
employs a property distance function (Venkatarajan and Braun 2001) to score the
similarity of two peptides. This is a far better solution as it takes into account the
level of degeneracy in the epitope sequence. The property distance function employs
five descriptors
E
1
-E
5
that were derived from 237 amino acid properties. The
property distance (PD) function for two amino acid sequences
A
and
B
of length
N
would be:
1
/
2
⎡
2
⎤
N
5
1
(
)
() ()
∑∑
=
PD
(
A
,
B
)
=
λ
E
A
−
E
B
(1)
⎢
⎥
j
j
i
j
i
N
⎣
⎦
i
1
j
=
1
