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OrthoInspector 2.0: Software and database updates

Benjamin Linard, Alexis Allot, Raphaël Schneider, Can Morel, Raymond Ripp, Marc Bigler, Julie D. Thompson, Olivier Poch, Odile Lecompte
2014 Computer applications in the biosciences : CABIOS  
We have added new functional tools and considerably extended the databases of pre-computed orthology/inparalogy relationships. Availability: Software and databases are freely available at  ...  We previously developed OrthoInspector, a software suite incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species.  ...  Eukaryote and prokaryote databases We have constructed 3 orthology databases with OrthoInspector (figure 1B).  ... 
doi:10.1093/bioinformatics/btu642 pmid:25273105 fatcat:tmq66b2rsndixamqs2vnbqeyly

OrthoInspector 3.0: open portal for comparative genomics

Yannis Nevers, Arnaud Kress, Audrey Defosset, Raymond Ripp, Benjamin Linard, Julie D Thompson, Olivier Poch, Odile Lecompte
2018 Nucleic Acids Research  
OrthoInspector is one of the leading software suites for orthology relations inference.  ...  The new website integrates original data exploration and visualization tools in an ergonomic interface.  ...  ACKNOWLEDGEMENTS We thank the Bio-statistics, Informatics and Complex System platform (BICS) and BISTRO bioinformatics platforms for informatics support and the European Grid Infrastructure for cloud computing  ... 
doi:10.1093/nar/gky1068 pmid:30380106 pmcid:PMC6323921 fatcat:dhx4n4gcxffrhf3fgcyf4geinm

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Clément-Marie Train, Natasha M Glover, Gaston H Gonnet, Adrian M Altenhoff, Christophe Dessimoz
2017 Bioinformatics  
Availability and Implementation: This new OMA 2.0 algorithm is used in the OMA database (http:// omabrowser.org) from the March 2017 release onwards, and can be run on custom genomes using OMA standalone  ...  version 2.0 and above (http://omabrowser.org/standalone).  ...  Acknowledgements We thank Georgina Bland for her contribution to the refinement for asymmetrically evolving paralogs, and Karina Zile for her thoughtful review of the article.  ... 
doi:10.1093/bioinformatics/btx229 pmid:28881964 pmcid:PMC5870696 fatcat:6nhrdpyjgjhsno5r5uwrosv64q

OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes

Woojin Kim, Ryan S. Underwood, Iva Greenwald, Daniel D. Shaye
2018 Genetics  
However, the efficacy of orthology prediction depends on the accuracy of gene-model predictions, an ongoing process, and orthology-prediction algorithms have also been updated over time.  ...  treatment of "legacy" genes no longer predicted by these programs; and the practical difficulties of updating due to encountering deprecated, changed, or retired gene identifiers.  ...  and encouragement.  ... 
doi:10.1534/genetics.118.301307 pmid:30120140 pmcid:PMC6216590 fatcat:2uiugitcnba7tikjumotdqr5ae

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

Bruno T. L. Nichio, Jeroniza Nunes Marchaukoski, Roberto Tadeu Raittz
2017 Frontiers in Genetics  
Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the  ...  and pointing to the problems that each one tries to address.  ...  The user account with a proteomes database to assist orthology researches (only in version 2.0).  ... 
doi:10.3389/fgene.2017.00165 pmid:29163633 pmcid:PMC5674930 fatcat:kl53wnq3unaxpoytoutf66olry

The Genome Sequence of the Eastern Woodchuck (Marmota monax) : A Preclinical Animal Model for Chronic Hepatitis B

Tyler S. Alioto, Fernando Cruz, Jèssica Gómez-Garrido, Miriam Triyatni, Marta Gut, Leonor Frias, Anna Esteve-Codina, Stephan Menne, Anna Kiialainen, Nadine Kumpesa, Fabian Birzele, Roland Schmucki (+2 others)
2019 G3: Genes, Genomes, Genetics  
This genome sequence and its annotation will enable further research in chronic hepatitis B and hepatocellular carcinoma and contribute to the understanding of immunological responses in the woodchuck.  ...  The result is a 2.63 Gigabase (Gb) assembly with a contig N50 of 74.5 kilobases (kb), scaffold N50 of 892 kb, and genome completeness of 99.2%.  ...  The consensus CDS models were then updated with untranslated regions (UTRs) and alternative exons through two rounds of PASA annotation updates.  ... 
doi:10.1534/g3.119.400413 pmid:31645421 pmcid:PMC6893209 fatcat:np2fmvqtcbgbbnivv4fkr22dt4

Standardized benchmarking in the quest for orthologs

Adrian M Altenhoff, Brigitte Boeckmann, Salvador Capella-Gutierrez, Daniel A Dalquen, Todd DeLuca, Kristoffer Forslund, Jaime Huerta-Cepas, Benjamin Linard, Cécile Pereira, Leszek P Pryszcz, Fabian Schreiber, Alan Sousa da Silva (+15 others)
2016 Nature Methods  
Altenhoff and Dessimoz 15 introduced a phylogenetic benchmark measuring the concordance between gene trees reconstructed from putative orthologs and undisputed species trees.  ...  the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.  ...  (also Supplementary Software).  ... 
doi:10.1038/nmeth.3830 pmid:27043882 pmcid:PMC4827703 fatcat:6jfxjkdbhjh2vn7ielkm3luhqe

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

2019 Nucleic Acids Research  
Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species  ...  Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species.  ...  We are very grateful to many anonymous reviewers for testing the server and offering valuable comments.  ... 
doi:10.1093/nar/gkz333 pmid:31053848 pmcid:PMC6602458 fatcat:7dq7sseswnfrtakv2w4bpkvuxa

SonicParanoid: fast, accurate and easy orthology inference

Salvatore Cosentino, Wataru Iwasaki, Russell Schwartz
2018 Bioinformatics  
OMA pairs 2.0 PANTHER 8.0 (all) OrthoInspector 1.30 OMA GETHOGs 2.0 OrthoFinder 2.0 (MSA, BLAST) SonicParanoid (sensitive) SonicParanoid (default) SonicParanoid (fast) Proteinortho Ensembl  ...  273 proteomes from the InParanoid8 database (Sonnhammer and Östlund, 2015) .  ... 
doi:10.1093/bioinformatics/bty631 pmid:30032301 fatcat:cmxmzps47vby5papmatr5q3foe

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Clément-Marie Train, Natasha M. Glover, Gaston H. Gonnet, Adrian M. Altenhoff, Christophe Dessimoz
2017
With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods.  ...  Motivation: Accurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous MAtrix).  ...  Acknowledgements We thank Georgina Bland for her contribution to the refinement for asymmetrically evolving paralogs, and Karina Zile for her thoughtful review of the article.  ... 
doi:10.3929/ethz-b-000191311 fatcat:zcxtq7vn3zcgldredqxcco4dvu

Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes

Philipp H. Schiffer, Etienne G.J. Danchin, Ann M. Burnell, Christopher J. Creevey, Simon Wong, Ilona Dix, Georgina O'Mahony, Bridget A. Culleton, Corinne Rancurel, Gary Stier, Elizabeth A. Martínez-Salazar, Aleksandra Marconi (+6 others)
2019 iScience  
and non-cryptobionts.  ...  To identify systems that may contribute to these striking abilities, we sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts  ...  ., and Lecompte, O. (2015). OrthoInspector 2.0: software and database updates. Bioinformatics 31, 447-448. Lucas-Lledó , J.I., and Lynch, M. (2009).  ... 
doi:10.1016/j.isci.2019.10.039 pmid:31759330 pmcid:PMC6889759 fatcat:ak6pc3qlvzaktk3dqaeg5obd7q

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Kerstin Howe, Philipp H. Schiffer, Julia Zielinski, Thomas Wiehe, Gavin K. Laird, John C. Marioni, Onuralp Soylemez, Fyodor Kondrashov, Maria Leptin
2016 Open Biology  
Leptin M. 2016 Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biol. 6: 160009. http://dx.  ...  We then used our own iPYTHON [62] script to sort data and calculated means, medians and errors in the R statistic software (R Core Team 2015).  ...  We loaded the inferred trees into DENDROSCOPE and employed this software to visualize connection between branches belonging to the same gene in both trees. Acknowledgements.  ... 
doi:10.1098/rsob.160009 pmid:27248802 pmcid:PMC4852459 fatcat:gtwcrbkak5gtjbpf4fd7d6pf4y

Structure and evolutionary history of a large family of NLR proteins in the zebrafish [article]

Kerstin Howe, Philipp Schiffer, Julia Zielinski, Thomas Wiehe, Gavin Laird, John Marioni, Onuralp Soylemez, Fyodor Kondrashov, Maria Leptin
2015 bioRxiv   pre-print
Animals and plants have evolved a range of mechanisms for recognizing noxious substances and organisms.  ...  Extensive duplication, loss of genes and domains, exon shuffling and gene conversion acting differentially on the NACHT and B30.2 domains have shaped the family.  ...  2.0 database (Linard et al. 2014 ) at http://lbgi.igbmc.fr/orthoinspector for 688 orthologs in published genomes and downloaded the corresponding sequence.  ... 
doi:10.1101/027151 fatcat:qqymo4nkyfak5eyhq72io4djki

Structure and evolutionary history of a large family of NLR proteins in the zebrafish [article]

Kerstin Howe, Philipp H Schiffer, Julia Zielinski, Thomas Wiehe, Gavin K Laird, John Marioni, Onuralp Soylemez, Fyodor Kondrashov, Maria Leptin
2015 bioRxiv   pre-print
NACHT- and Leucine-Rich-Repeat-containing domain (NLR) proteins act as cytoplasmic sensors for pathogen- and danger-associated molecular patterns and are found throughout the plant and animal kingdoms.  ...  We have analysed the expanded NLR gene family in zebrafish, which contains 368 genes, and studied its evolutionary history.  ...  and!Giuliano!Crispatzu!for!some!early!work!on!this!project!and! Jonathan!Wood!for!verifying!genomic!locations!of!assembly!components.  ... 
doi:10.1101/022061 fatcat:jln6nerwvze43awct7euq6ivgy

Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling

Yannis Nevers, Megana K. Prasad, Laetitia Poidevin, Kirsley Chennen, Alexis Allot, Arnaud Kress, Raymond Ripp, Julie D. Thompson, Hélène Dollfus, Olivier Poch, Odile Lecompte
2017 Molecular biology and evolution  
By combining gene-centric and species-oriented analyses, this work reveals new ciliary and ciliopathy gene candidates and provides clues about the evolution of ciliary processes in the eukaryotic domain  ...  Cilia (flagella) are important eukaryotic organelles, present in the Last Eukaryotic Common Ancestor, and are involved in cell motility and integration of extracellular signals.  ...  We thank Dr Séverine B€ ar (University of Strasbourg) for providing the hTERT-RPE1 cells, and the BICS and BISTRO bioinformatics platforms for informatics support.  ... 
doi:10.1093/molbev/msx146 pmid:28460059 pmcid:PMC5850483 fatcat:ooox2wa2ezcffdwlpxolr4irlq