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An approach of orthology detection from homologous sequences under minimum evolution

Cited 24 time in Web of Science Cited 25 time in Scopus
Authors
Kim, Kyung Mo; Sung, Samsun; Caetano-Anolle´ s, Gustavo; Han, Jae Yong; Kim, Heebal
Issue Date
2008
Publisher
Oxford University Press
Citation
Nucleic Acids Research, vol.36 no.17, e110
Description
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
In the field of phylogenetics and comparative
genomics, it is important to establish orthologous
relationships when comparing homologous
sequences. Due to the slight sequence dissimilarity
between orthologs and paralogs, it is prone to
regarding paralogs as orthologs. For this reason,
several methods based on evolutionary distance,
phylogeny and BLAST have tried to detect orthologs
with more precision. Depending on their algorithmic
implementations, each of these methods
sometimes has increased false negative or false
positive rates. Here, we developed a novel algorithm
for orthology detection that uses a distance
method based on the phylogenetic criterion of minimum
evolution. Our algorithm assumes that sets
of sequences exhibiting orthologous relationships
are evolutionarily less costly than sets that include
one or more paralogous relationships. Calculation
of evolutionary cost requires the reconstruction
of a neighbor-joining (NJ) tree, but calculations are
unaffected by the topology of any given NJ tree.
Unlike tree reconciliation, our algorithm appears
free from the problem of incorrect topologies of
species and gene trees. The reliability of the algorithm
was tested in a comparative analysis with two
other orthology detection methods using 95 manually
curated KOG datasets and 21 experimentally
verified EXProt datasets. Sensitivity and specificity
estimates indicate that the concept of minimum
evolution could be valuable for the detection of orthologs.
ISSN
0305-1048
Language
English
URI
https://hdl.handle.net/10371/100259
DOI
https://doi.org/10.1093/nar/gkn485
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