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OJBTM
Online Journal of Bioinformatics ©
Volume 10 (2): 259-279, 2009.
In Silico analysis of translation
initiation sites from P. falciparum
Balakota Reddy Patakottu1,
Chandrasekhar Mamidipally2,
Swati Patankar1, Santosh
Noronha1,2
1Department of Biosciences and
Bioengineering, 2Chemical
Engineering, Indian Institute of Technology, Mumbai, India.
ABSTRACT
Patakottu BR, Mamidipally C, Patankar
S, Noronha
S, In Silico analysis
of translation initiation sites from P.
falciparum, Online J Bioinformatics, 10
(2): 259-279, 2009. The human malaria
parasite Plasmodium
falciparum has a biased genome
composition of 80-90% AT. Due to this bias and the unusually long
length of untranslated regions in parasite
mRNAs, the number of
putative Translation Initiation Sites (TIS) is higher than other
eukaryotes and
raises the question of which sequence features distinguish true TIS
from poorly
recognized AUG codons. To address this
question we
computationally identified sequence features that can predict true TIS
in P. falciparum. TIS were predicted using
feature generation
and standard machine learning classifiers and a dataset containing 61
experimentally well characterized TIS. Eighteen features were
identified which
classify TIS with an accuracy of 98% and a true positive prediction
rate of
87%. These 18 features reflect the parasite genome composition and
include
bases at the -1,-2, -3, -4 positions, AT-rich features and abundant codons. Annotated genes were analyzed using our
TIS
prediction model, and these gave high accuracy with reduced true
positive rates
in different stages of the parasite life cycle. In this report we also
predict
the experimentally validated alternate translation initiation site of
the Pfgrasp gene. This work is the first to
use genomic and
proteomic data to predict TIS in P. falciparum
and has
implications for further studies on translation initiation in the
malaria
parasite.
Key Words: Malaria,
Translation, Initiation, P falciparum