Proteinortho : Detection of (Co-)orthologs in large-scale analysis
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TLDR
Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.Abstract:
Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.read more
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Genome evolution across 1,011 Saccharomyces cerevisiae isolates
Jackson Peter,Matteo De Chiara,Anne Friedrich,Jia-Xing Yue,David Pflieger,Anders Bergström,Anastasie Sigwalt,Benjamin Barré,Kelle C. Freel,Agnès Llored,Corinne Cruaud,Karine Labadie,Jean-Marc Aury,Benjamin Istace,Kevin Lebrigand,Pascal Barbry,Stefan Engelen,Arnaud Lemainque,Patrick Wincker,Patrick Wincker,Gianni Liti,Joseph Schacherer +21 more
TL;DR: Whole-genome sequencing and phenotyping of 1,011 natural isolates of the yeast Saccharomyces cerevisiae reveal its evolutionary history, including a single out-of-China origin and multiple domestication events, and provides a framework for genotype–phenotype studies in this model organism.
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OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species
TL;DR: A web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters and allows for a customized search of clusters of specific genes through key words or BLAST is reported.
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Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals
Kate L. Ormerod,David L. A. Wood,Nancy Lachner,Shaan L. Gellatly,Joshua Daly,Jeremy Parsons,Cristiana Gomes de Oliveira Dal'Molin,Robin W. Palfreyman,Lars K. Nielsen,Mark E. Cooper,Mark Morrison,Philip M. Hansbro,Philip Hugenholtz +12 more
TL;DR: The first whole genome exploration of the Bacteroidales family S24-7 is provided, for which the name “Candidatus Homeothermaceae” is proposed, using 30 population genomes extracted from fecal samples of four different animal hosts.
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Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile.
Uwe Groß,Elzbieta Brzuszkiewicz,Katrin Gunka,Jessica Starke,Thomas Riedel,Boyke Bunk,Cathrin Spröer,Daniela Wetzel,Anja Poehlein,Cynthia Maria Chibani,Wolfgang Bohne,Jörg Overmann,Ortrud Zimmermann,Rolf Daniel,Heiko Liesegang +14 more
TL;DR: Findings show that evolutionary events based on horizontal gene transfer occur within an ongoing CDI and contribute to the adaptation of the species by the introduction of new genes into the genomes.
Journal ArticleDOI
Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
Ronald P. de Vries,Robert Riley,Ad Wiebenga,Guillermo Aguilar-Osorio,Sotiris Amillis,Cristiane Uchima,Gregor Anderluh,Mojtaba Asadollahi,Marion Askin,Marion Askin,Kerrie Barry,Evy Battaglia,Özgür Bayram,Özgür Bayram,Tiziano Benocci,Susanna A. Braus-Stromeyer,Camila Caldana,David Cánovas,David Cánovas,Gustavo C. Cerqueira,Fusheng Chen,Wanping Chen,Cindy Choi,Alicia Clum,Renato Augusto Corrêa dos Santos,André Damasio,George Diallinas,Tamás Emri,Erzsébet Fekete,Michel Flipphi,Susanne Freyberg,Antonia Gallo,Christos Gournas,Rob Habgood,Matthieu Hainaut,María Harispe,Bernard Henrissat,Bernard Henrissat,Bernard Henrissat,Kristiina Hildén,Ryan Hope,Abeer Hossain,Eugenia Karabika,Eugenia Karabika,Levente Karaffa,Zsolt Karányi,Nada Kraševec,Alan Kuo,Harald Kusch,Kurt LaButti,Ellen Lagendijk,Alla Lapidus,Alla Lapidus,Anthony Levasseur,Erika Lindquist,Anna Lipzen,Antonio F. Logrieco,Andrew MacCabe,Miia R. Mäkelä,Iran Malavazi,Petter Melin,Vera Meyer,Natalia Mielnichuk,Natalia Mielnichuk,Márton Miskei,Ákos Molnár,Giuseppina Mulè,Chew Yee Ngan,Margarita Orejas,Erzsébet Orosz,Erzsébet Orosz,Jean Paul Ouedraogo,Jean Paul Ouedraogo,Karin M. Overkamp,Hee-Soo Park,Giancarlo Perrone,François Piumi,François Piumi,Peter J. Punt,Arthur F. J. Ram,Ana Ramón,Stefan Rauscher,Eric Record,Diego Mauricio Riaño-Pachón,Vincent Robert,Julian Röhrig,Roberto Ruller,Asaf Salamov,Nadhira Salih,Nadhira Salih,Rob Samson,Erzsébet Sándor,Manuel Sanguinetti,Tabea Schütze,Tabea Schütze,Kristina Sepčić,Ekaterina Shelest,Gavin Sherlock,Vicky Sophianopoulou,Fabio M. Squina,Hui Sun,Antonia Susca,Richard B. Todd,Adrian Tsang,Shiela E. Unkles,Nathalie van de Wiele,Diana van Rossen-Uffink,Juliana Velasco de Castro Oliveira,Tammi Camilla Vesth,Jaap Visser,Jae-Hyuk Yu,Miaomiao Zhou,Mikael Rørdam Andersen,David B. Archer,Scott E. Baker,Isabelle Benoit,Isabelle Benoit,Axel A. Brakhage,Gerhard H. Braus,Reinhard Fischer,Jens Christian Frisvad,Gustavo H. Goldman,Jos Houbraken,Berl R. Oakley,István Pócsi,Claudio Scazzocchio,Claudio Scazzocchio,Bernhard Seiboth,Patricia A. vanKuyk,Patricia A. vanKuyk,Jennifer R. Wortman,Paul S. Dyer,Igor V. Grigoriev +132 more
TL;DR: In this article, a comparative genomics and experimental study of the aspergilli genus is presented, which allows for the first time a genus-wide view of the biological diversity of the Aspergillus and in many, but not all, cases linked genome differences to phenotype.
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