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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, Onl
J Bioinform, 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.