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Di L, Balesano A, Jordan S, Shi SM. The Role of Alcohol Dehydrogenase in Drug Metabolism: Beyond Ethanol Oxidation. AAPS JOURNAL 2021; 23:20. [DOI: 10.1208/s12248-020-00536-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023]
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Abstract
Alcohol consumption has long been a part of human culture. However, alcohol consumption levels and alcohol consumption patterns are associated with chronic diseases. Overall, light and moderate alcohol consumption (up to 14 g per day for women and up to 28 g per day for men) may be associated with reduced mortality risk, mainly due to reduced risks for cardiovascular disease and type-2 diabetes. However, chronic heavy alcohol consumption and alcohol abuse lead to alcohol-use disorder, which results in physical and mental diseases such as liver disease, pancreatitis, dementia, and various types of cancer. Risk factors for alcohol-use disorder are largely unknown. Alcohol-use disorder and frequent heavy drinking have detrimental effects on personal health.
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3
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Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Warwick Vesztrocy A, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C. OMA standalone: orthology inference among public and custom genomes and transcriptomes. Genome Res 2019; 29:1152-1163. [PMID: 31235654 PMCID: PMC6633268 DOI: 10.1101/gr.243212.118] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/24/2019] [Indexed: 11/24/2022]
Abstract
Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0.
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Affiliation(s)
- Adrian M Altenhoff
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Jeremy Levy
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, United Kingdom.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Magdalena Zarowiecki
- Genomics England, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Bartłomiej Tomiczek
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom.,Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Alex Warwick Vesztrocy
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Daniel A Dalquen
- Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Steven Müller
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Natasha M Glover
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - David Dylus
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Department of Computer Science, University College London, London WC1E 6BT, United Kingdom
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4
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Biondi E, Benner SA. Artificially Expanded Genetic Information Systems for New Aptamer Technologies. Biomedicines 2018; 6:E53. [PMID: 29747381 PMCID: PMC6027400 DOI: 10.3390/biomedicines6020053] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/04/2018] [Accepted: 05/06/2018] [Indexed: 01/04/2023] Open
Abstract
Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS) that adds independently replicating nucleotide “letters” to the evolving “alphabet”.
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Affiliation(s)
- Elisa Biondi
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL 32615, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL 32615, USA.
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5
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Polimanti R, Gelernter J. ADH1B: From alcoholism, natural selection, and cancer to the human phenome. Am J Med Genet B Neuropsychiatr Genet 2018; 177:113-125. [PMID: 28349588 PMCID: PMC5617762 DOI: 10.1002/ajmg.b.32523] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022]
Abstract
The ADH1B (Alcohol Dehydrogenase 1B (class I), Beta Polypeptide) gene and its best-known functional alleles, Arg48His (rs1229984, ADH1B*2) and Arg370Cys (rs2066702, ADH1B*3), have been investigated in relation to many phenotypic traits; most frequently including alcohol metabolism and alcohol drinking behaviors, but also human evolution, liver function, cancer, and, recently, the comprehensive human phenome. To understand ADH1B functions and consequences, we provide here a bioinformatic analysis of its gene regulation and molecular functions, literature review of studies focused on this gene, and a discussion regarding future research perspectives. Certain ADH1B alleles have large effects on alcohol metabolism, and this relationship particularly encourages further investigations in relation to alcoholism and alcohol-associated cancer to understand better the mechanisms by which alcohol metabolism contributes to alcohol abuse and carcinogenesis. We also observed that ADH1B has complex mechanisms that regulate its expression across multiple human tissues, and these may be involved in cardiac and metabolic traits. Evolutionary data strongly suggest that the selection signatures at the ADH1B locus are primarily related to effects other than those on alcohol metabolism. This is also supported by the involvement of ADH1B in multiple molecular pathways and by the findings of our recent phenome-wide association study. Accordingly, future studies should also investigate other functions of ADH1B potentially relevant for the human phenome. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Renato Polimanti
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
- Department of Genetics, Yale School of Medicine, West Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, West Haven, CT, USA
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6
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Alcalde M. When directed evolution met ancestral enzyme resurrection. Microb Biotechnol 2016; 10:22-24. [PMID: 27863072 PMCID: PMC5270717 DOI: 10.1111/1751-7915.12452] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/09/2016] [Indexed: 11/29/2022] Open
Abstract
The directed evolution of ancestral ‐resurrected‐ enzymes can give a new twist in protein engineering approaches towards more versatile and robust biocatalysts.
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Affiliation(s)
- Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049, Madrid, Spain
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7
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Retson TA, Sterling R, Van Bockstaele EJ. Alcohol-induced dysregulation of stress-related circuitry: The search for novel targets and implications for interventions across the sexes. Prog Neuropsychopharmacol Biol Psychiatry 2016; 65:252-9. [PMID: 26006055 PMCID: PMC4656147 DOI: 10.1016/j.pnpbp.2015.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/15/2015] [Accepted: 05/15/2015] [Indexed: 01/22/2023]
Abstract
While the ability to process fermented fruits and alcohols was once an adaptive trait that improved nutrition and quality of life, the availability and prevalence of high potency alcoholic drinks has contributed to alcohol abuse disorders in a vulnerable portion of the population. Although the neural reward systems take part in the initial response to alcohol, negative reinforcement and stress, which are normally adaptive responses, can intersect to promote continued alcohol use at all stages of the addiction cycle. Eventually a point is reached where these once adaptive responses become dysregulated resulting in uncontrolled intake that constitutes a clinically important condition termed alcohol use disorder (AUD). Current research is targeted at both the behavioral and molecular adaptations in AUDs in an effort to better develop novel approaches to intervention. In this review, historical context is provided demonstrating the societal burden of alcohol use and abuse disorders. The importance of gender in the mechanism of action of alcohol is discussed. Finally, the impact of alcohol on stress-related circuitry, uncovered by preclinical research, is outlined to provide insight into potential novel pharmacological approaches to the treatment of AUD.
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Affiliation(s)
- T. A. Retson
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
| | - R.C. Sterling
- Department of Psychiatry and Human Behavior, Thomas Jefferson University, Philadelphia, PA 19107
| | - E. J. Van Bockstaele
- Department of Pharmacology and Physiology, College of Medicine, Drexel University, Philadelphia, PA 19102
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Östberg LJ, Persson B, Höög JO. The mammalian alcohol dehydrogenase genome shows several gene duplications and gene losses resulting in a large set of different enzymes including pseudoenzymes. Chem Biol Interact 2015; 234:80-4. [DOI: 10.1016/j.cbi.2014.11.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/19/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
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Hockings KJ, Bryson-Morrison N, Carvalho S, Fujisawa M, Humle T, McGrew WC, Nakamura M, Ohashi G, Yamanashi Y, Yamakoshi G, Matsuzawa T. Tools to tipple: ethanol ingestion by wild chimpanzees using leaf-sponges. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150150. [PMID: 26543588 PMCID: PMC4632552 DOI: 10.1098/rsos.150150] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/14/2015] [Indexed: 05/18/2023]
Abstract
African apes and humans share a genetic mutation that enables them to effectively metabolize ethanol. However, voluntary ethanol consumption in this evolutionary radiation is documented only in modern humans. Here, we report evidence of the long-term and recurrent ingestion of ethanol from the raffia palm (Raphia hookeri, Arecaceae) by wild chimpanzees (Pan troglodytes verus) at Bossou in Guinea, West Africa, from 1995 to 2012. Chimpanzees at Bossou ingest this alcoholic beverage, often in large quantities, despite an average presence of ethanol of 3.1% alcohol by volume (ABV) and up to 6.9% ABV. Local people tap raffia palms and the sap collects in plastic containers, and chimpanzees use elementary technology-a leafy tool-to obtain this fermenting sap. These data show that ethanol does not act as a deterrent to feeding in this community of wild apes, supporting the idea that the last common ancestor of living African apes and modern humans was not averse to ingesting foods containing ethanol.
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Affiliation(s)
- Kimberley J. Hockings
- Centre for Research in Anthropology (CRIA-FCSH/UNL), Lisbon 1069-061, Portugal
- Anthropology Centre for Conservation, Environment and Development, Oxford Brookes University, Oxford OX3 0BP, UK
- Author for correspondence: Kimberley J. Hockings e-mail:
| | | | - Susana Carvalho
- Center for the Advanced Study of Hominid Paleobiology, George Washington University, Washington DC, 20052, USA
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior, Universidade do Algarve, Faro 8005-139, Portugal
| | - Michiko Fujisawa
- Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
- Center for Southeast Asian Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tatyana Humle
- School of Anthropology and Conservation, University of Kent, Canterbury CT2 7NR, UK
| | - William C. McGrew
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Miho Nakamura
- Wildlife Research Center, Kyoto University, Kyoto 606-8203, Japan
| | - Gaku Ohashi
- Wildlife Research Center, Kyoto University, Kyoto 606-8203, Japan
- Japan Monkey Centre, Inuyama 484-0081, Japan
- Chubu University, Kasugai 487-8501, Japan
| | - Yumi Yamanashi
- Wildlife Research Center, Kyoto University, Kyoto 606-8203, Japan
| | - Gen Yamakoshi
- Center for African Area Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tetsuro Matsuzawa
- Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
- Japan Monkey Centre, Inuyama 484-0081, Japan
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Winnier DA, Fourcaudot M, Norton L, Abdul-Ghani MA, Hu SL, Farook VS, Coletta DK, Kumar S, Puppala S, Chittoor G, Dyer TD, Arya R, Carless M, Lehman DM, Curran JE, Cromack DT, Tripathy D, Blangero J, Duggirala R, Göring HHH, DeFronzo RA, Jenkinson CP. Transcriptomic identification of ADH1B as a novel candidate gene for obesity and insulin resistance in human adipose tissue in Mexican Americans from the Veterans Administration Genetic Epidemiology Study (VAGES). PLoS One 2015; 10:e0119941. [PMID: 25830378 PMCID: PMC4382323 DOI: 10.1371/journal.pone.0119941] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 02/04/2015] [Indexed: 01/01/2023] Open
Abstract
Type 2 diabetes (T2D) is a complex metabolic disease that is more prevalent in ethnic groups such as Mexican Americans, and is strongly associated with the risk factors obesity and insulin resistance. The goal of this study was to perform whole genome gene expression profiling in adipose tissue to detect common patterns of gene regulation associated with obesity and insulin resistance. We used phenotypic and genotypic data from 308 Mexican American participants from the Veterans Administration Genetic Epidemiology Study (VAGES). Basal fasting RNA was extracted from adipose tissue biopsies from a subset of 75 unrelated individuals, and gene expression data generated on the Illumina BeadArray platform. The number of gene probes with significant expression above baseline was approximately 31,000. We performed multiple regression analysis of all probes with 15 metabolic traits. Adipose tissue had 3,012 genes significantly associated with the traits of interest (false discovery rate, FDR ≤ 0.05). The significance of gene expression changes was used to select 52 genes with significant (FDR ≤ 10(-4)) gene expression changes across multiple traits. Gene sets/Pathways analysis identified one gene, alcohol dehydrogenase 1B (ADH1B) that was significantly enriched (P < 10(-60)) as a prime candidate for involvement in multiple relevant metabolic pathways. Illumina BeadChip derived ADH1B expression data was consistent with quantitative real time PCR data. We observed significant inverse correlations with waist circumference (2.8 x 10(-9)), BMI (5.4 x 10(-6)), and fasting plasma insulin (P < 0.001). These findings are consistent with a central role for ADH1B in obesity and insulin resistance and provide evidence for a novel genetic regulatory mechanism for human metabolic diseases related to these traits.
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Affiliation(s)
- Deidre A. Winnier
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Marcel Fourcaudot
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Luke Norton
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Muhammad A. Abdul-Ghani
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Shirley L. Hu
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Vidya S. Farook
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Dawn K. Coletta
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Satish Kumar
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Sobha Puppala
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Geetha Chittoor
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Thomas D. Dyer
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Rector Arya
- Division of Endocrinology and Diabetes, Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Melanie Carless
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Donna M. Lehman
- Division of Clinical Epidemiology, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Joanne E. Curran
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Douglas T. Cromack
- Division of Orthopedics, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- South Texas Veterans Health Care System, San Antonio, TX, United States of America
| | - Devjit Tripathy
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- South Texas Veterans Health Care System, San Antonio, TX, United States of America
| | - John Blangero
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | | | - Harald H. H. Göring
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Ralph A. DeFronzo
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- South Texas Veterans Health Care System, San Antonio, TX, United States of America
| | - Christopher P. Jenkinson
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
- South Texas Veterans Health Care System, San Antonio, TX, United States of America
- * E-mail:
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11
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Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res 2014; 43:D240-9. [PMID: 25399418 PMCID: PMC4383958 DOI: 10.1093/nar/gku1158] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org.
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Affiliation(s)
- Adrian M Altenhoff
- University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
| | - Nives Škunca
- University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
| | - Natasha Glover
- University College London, Gower Street, London WC1E 6BT, UK Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium
| | | | - Anna Sueki
- University College London, Gower Street, London WC1E 6BT, UK
| | - Ivana Piližota
- University College London, Gower Street, London WC1E 6BT, UK
| | - Kevin Gori
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Steven Müller
- University College London, Gower Street, London WC1E 6BT, UK
| | | | - Gaston H Gonnet
- Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
| | - Christophe Dessimoz
- University College London, Gower Street, London WC1E 6BT, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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12
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Soares I, Goios A, Amorim A. Sequence comparison alignment-free approach based on suffix tree and L-words frequency. ScientificWorldJournal 2012; 2012:450124. [PMID: 22997494 PMCID: PMC3444837 DOI: 10.1100/2012/450124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/05/2012] [Indexed: 11/17/2022] Open
Abstract
The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.
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Affiliation(s)
- Inês Soares
- Faculdade de Ciências da Universidade do Porto, 4169 Porto, Portugal.
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