Biology Reference
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(“molecular function”), and specific biological role/s (“biological
process”) of each transcript for which sufficient data were available. More
specific inferences of biological function were achieved using homology-
based comparisons among functional orthologues and/or conserved
biological pathways (e.g. oxidative phosphorylation) defined in the Kyoto
Encyclopedia of Genes and Genomes (KEGG) (
www.kegg.com
).
However, although comparison using the KEGG database allows the
identification of the functions of thousands of orthologous sequences, this
approach is only applicable to conserved genes involved in the same
biological function in a broad range of organisms (e.g. metabolic, DNA
replication or cell signaling pathways). Using this approach, function
could be predicted for
12.5% (2500) of the genes in
A. suum
.
To increase the number of functionally annotated genes in the
A. suum
genome, the amino acid sequence inferred from each coding domain was
compared by BLASTp with protein sequences available in a wide range of
databases. Numerous databases can be utilized for this purpose. For
A. suum
, substantial functional information was inferred based on
homology with genes encoded by
C. elegans
and linked to extensive func-
tional/phenotypic data archived in WormBase (
www.wormbase.org
) rep-
resenting decades of experimental investigations of
C. elegans
. Given the
relatively close biological relationship between
A. suum
and
C. elegans
,this
database clearly represented the richest source of data to infer the function
of each predicted gene. In addition to this resource, functional information
could also be collected based on similar comparisons to other model
organisms, such as
D. melonagaster
32
and
Mus musculus
,
33
and/or homology
to sequences contained in curated general or specific protein data-
bases, including UniProt,
34
SwissProt or TrEMBL
35
as well as MEROPS
36
(peptidases), KS-Sarfari (kinases) and GPCR-Sarfari (G-protein-coupled
receptors) (
http://www.sarfari.org
), and the Transporter Classification
DataBase (TCDB).
37
In addition to these classifications, because such proteins are known to
play key roles in the host
w
parasite interaction, including in evasion or
modulation of the host immune responses and degradation of host tissues,
we predicted excretory/secretory (ES) proteins for
A. suum
. First, using the
program Phobius,
38
signal peptides, inferred to allow trafficking across the
cell membrane, were predicted by neural network and Hidden Markov
Modeling. These molecules were then compared by BLASTp analysis to
curated proteins in the signal peptide database (SPD)
39
and in an ES
database containing published proteomic data for
B. malayi
,
40,41
Meloido-
gyne incognita
,
42
and
Schistosoma mansoni
.
43
A peptide was classified as
being a representative of the
A. suum
secretome if it encoded a signal
peptide and was supported by having an homologue in the SPD database
and/or the ES proteomes predicted for other parasitic helminths.
e
