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Sonnhammer ELL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C. Big data and other challenges in the quest for orthologs. Bioinformatics 2014; 30:2993-8. [PMID: 25064571 PMCID: PMC4201156 DOI: 10.1093/bioinformatics/btu492] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/25/2014] [Accepted: 07/16/2014] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. AVAILABILITY AND IMPLEMENTATION All such materials are available at http://questfororthologs.org.
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Affiliation(s)
- Erik L L Sonnhammer
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London
| | - Toni Gabaldón
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London
| | - Alan W Sousa da Silva
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK
| | - Maria Martin
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK
| | - Marc Robinson-Rechavi
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London
| | - Brigitte Boeckmann
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK
| | - Paul D Thomas
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK
| | - Christophe Dessimoz
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London
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