Prasetya, Hendra
Date:
2011
Abstract:
Bioinformatics as a
recent improvement of knowledge has made an interest for scientist to
collect and analyze data to provide the best estimate of the true
phylogeny. The objective of this research is to construct and compare
the phylogenetic tree of Neighbour Joining (NJ) based on different
models (Kimura 2-Parameters and Jukes-Cantor) and to find out which
model is more reliable on constructing NJ’s tree. In order to build the
tree, reliable set of data is conducted from D-loop mtDNA sequences that
is available in Gen Bank. The nucleotide sequences come from Bison
bison (American bison), Bos taurus (European cow such as Shorthorn), Bos
indicus (zebu breeds), Bos grunniens mutus (one of subspecies of cow),
and Capra hircus (species of goat). The reliability of each models was
measured using the Felsentein’s bootstrap method. The whole bootstrap
process for each models was repeated 1.000, 5.000, and 10.000 times to
detect its reliability. The performance was measured on the basis of the
consistency of the topology relationship, the stability of nodes, the
consistency of bootstrap confidence level (PB), standard error of
distance, change of PB from (1.000-5.000) to (5.000-1.000),
computational time, and BIC score. NJ’s phylogenetic tree with kimura
2-parameters and jukes cantor model have a good node stability and is
also generally successful in representing topological relationships
between taxa. The increasing of bootstrap replication number in common
will increase the consistency of bootstrap confidence value ( . It means
both models have a good reliability. But, when the number of sequences
is large and the extent of sequence divergence is low, it is generally
difficult to construct the tree by any models. In conclusion, Kimura
2-Parameters has a better performance than Jukes-Cantor.
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