Information Technology Reference
In-Depth Information
where λ is the eigenvalue of the
j
th
E
component,
E
j
(A
i
) is the
E
j
value for the
amino acid in the
i
th position from sequence
A
, and
E
j
(
B
i
) is the
E
j
value for the
amino acid in the
i
th position from sequence B.
For any given novel protein sequence, the PD function is used to determine the
similarity measure of the novel protein sequence against all same length
subsequences in SDAP. The results are then ranked and displayed together with a
histogram to the user. The histogram aids the user in determining the significance of
the results. If a match is detected that has a much lower similarity measure than the
rest of the matches, the match may be significant and should be analysed further. The
PD method has been successfully used to detect cross-reactivity among allergens on
the basis that they share similar epitopes. Similar to other allergen databases,
downloading of the data is not supported. This is a major problem for
bioinformaticians who require sets of data for further analysis.
j
5.2.3.4 Allergome
Allergome (Mari and Riccioli 2004) was started in 2000 and released in February
2003. All the records are manually curated by experts. The primary data source for
Allergome is literature published since the early 1960s. As of February 2007,
Allergome contains more than 9000 references categorized by topics and allergens
(Mari, Scala, Palazzo, Ridolfi, Zennaro , and Carabella 2007).
Not all the allergens in Allergome are found in the IUIS list of allergens and
records in Allergome clearly demarcate which records are in the IUIS list. Allergens
that are not in the IUIS list are carefully checked to ensure that they are valid
allergens prior to the addition in Allergome.
Allergome records integrate literature data and are therefore very information-
rich. Each record may contain the allergen name, common names, biological
functions, links to primary sequence information, links to PDB structures, sequence
motifs, source of allergen, tissue source of allergen, route of exposure, allergen
isoforms, prevalence of allergy, references, molecular weight, sequence homologues,
posttranslational modifications, test of allergenicity both
in viv
o and
in vitro
, cross-
reactivity, recombinant forms of the allergen, and literature references.
Allergome has user-friendly search facilities. A quick search using keywords
enables users to filter the results in several ways to display, for example, only IUIS-
listed allergens. The advanced search allows users to search specific fields using
Boolean modifiers. Similar to the quick search, users can filter their results. In
addition to the search facilities, Allergome provides lists of allergens sorted by
categories.
Download facilities are also lacking in Allergome. This is particularly dire in the
case of Allergome because the richness of the data cannot be easily exploited for
large-scale bioinformatics analysis. This is further compounded by the fact that
Allergome does not contain any computational tools that could take advantage of
these data.
