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February 2009

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[Beg-evodevo] Accurate Identification of Orthologous Segments among multiple genomes [Bioinformatics. 2009] - PubMed Result
by Cindy Martens 07 Feb '09

07 Feb '09

In this paper they propose a new algorithm to detect orthologous segments and compare the accuracy with other existing algoritms like _*ADHoRe*_.* *cheers, Cindy* -------------------------------------------------------------------------------------------------- Accurate Identification of Orthologous Segments among Multiple Genomes.* *Hachiya T* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Hachi…>, *Osana Y* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Osana…>, *Popendorf K* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Popen…>, *Sakakibara Y* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Sakak…>. 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(a)dna.bio.keio.ac.jp SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Bioinformatics. <javascript:AL_get(this, 'jour', 'Bioinformatics.');> 2009 Feb 2. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/19188192?dopt=Abstract -- ================================================================== 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(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] writing | ben fry » F* Everything, We’re Doing 44 Vertebrates
by Klaas Vandepoele 06 Feb '09

06 Feb '09

http://benfry.com/writing/archives/269 -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/

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