In this paper they
propose a new algorithm to detect orthologous segments and compare the
accuracy with other existing algoritms like ADHoRe.
cheers,
Cindy
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Accurate Identification of Orthologous Segments among Multiple Genomes.
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Department of Biosciences and Informatics,
Keio University, Japan.
MOTIVATION: The accurate detection of orthologous segments (also
referred to as syntenic segments) plays a key role in comparative
genomics, as it is useful for inferring genome rearrangement scenarios
and computing whole genome alignments. Although a number of algorithms
for detecting orthologous segments have been proposed, none of them
contain a framework for optimizing their parameter values. METHODS: In
the present study, we propose an algorithm, named OSfinder (Orthologous
Segment finder), which uses a novel scoring scheme based on stochastic
models. OSfinder takes as input the positions of short homologous
regions (also referred to as anchors) and explicitly discriminates
orthologous anchors from nonorthologous anchors by using Markov chain
models which represent respective geometric distributions of lengths of
orthologous and nonorthologous anchors. Such stochastic modeling makes
it possible to optimize parameter values by maximizing the likelihood
of the input dataset, and to automate the setting of the optimal
parameter values. RESULTS: We validated the accuracies of orthology
mapping algorithms on the basis of their consistency with the orthology
annotation of genes. Our evaluation tests using mammalian and bacterial
genomes demonstrated that OSfinder shows higher accuracy than previous
algorithms. AVAILABILITY: The OSfinder software was implemented as a
C++ program. The software is freely available at
http://osfinder.dna.bio.keio.ac.jp under the GNU General Public
License. CONTACT: hacchy@dna.bio.keio.ac.jp SUPPLEMENTARY INFORMATION:
Supplementary data are available at Bioinformatics online.
Bioinformatics.
2009 Feb 2. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/19188192?dopt=Abstract
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Cindy Martens
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
Tel: +32 (0)9 331 38 22
Fax: +32 (0)9 331 38 09
E-mail: cindy.martens@psb.vib-ugent.be
Website: http://bioinformatics.psb.ugent.be/
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