- Genome3D: exploiting structure to help users understand their sequences. [PMID: 25348407]
Tony E Lewis, Ian Sillitoe, Antonina Andreeva, Tom L Blundell, Daniel W A Buchan, Cyrus Chothia, Domenico Cozzetto, José M Dana, Ioannis Filippis, Julian Gough, David T Jones, Lawrence A Kelley, Gerard J Kleywegt, Federico Minneci, Jaina Mistry, Alexey G Murzin, Bernardo Ochoa-Montaño, Matt E Oates, Marco Punta, Owen J L Rackham, Jonathan Stahlhacke, Michael J E Sternberg, Sameer Velankar, Christine Orengo
Nucleic acids research 2015:43(Database issue)
2 Citations (Google Scholar as of 2016-03-25)
Abstract: Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
- Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. [PMID: 23203986]
Tony E Lewis, Ian Sillitoe, Antonina Andreeva, Tom L Blundell, Daniel W A Buchan, Cyrus Chothia, Alison Cuff, Jose M Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T Jones, Lawrence A Kelley, Gerard J Kleywegt, Federico Minneci, Alex Mitchell, Alexey G Murzin, Bernardo Ochoa-Montaño, Owen J L Rackham, James Smith, Michael J E Sternberg, Sameer Velankar, Corin Yeats, Christine Orengo
Nucleic acids research 2013:41(Database issue)
29 Citations (Google Scholar as of 2016-01-18)
Abstract: Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).
- Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. [PMID: 20813045]
Thomas M Asbury, Matt Mitman, Jijun Tang, W Jim Zheng
BMC bioinformatics 2010:11
11 Citations (Google Scholar as of 2016-01-18)
Abstract: New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation. We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order to integrate and visualize large volume of data, novel statistical and mathematical approaches have been developed to reduce the size of the data. To our knowledge, this is the first such tool developed that can visualize human genome in three-dimension. We describe here the major features of Genome3D and discuss our multi-scale data framework using a representative basic physical model. We then demonstrate many of the issues and benefits of multi-resolution data integration. Genome3D is a software visualization tool that explores a wide range of structural genomic and epigenetic data. Data from various sources of differing scales can be integrated within a hierarchical framework that is easily adapted to new developments concerning the structure of the physical genome. In addition, our tool has a simple annotation mechanism to incorporate non-structural information. Genome3D is unique is its ability to manipulate large amounts of multi-resolution data from diverse sources to uncover complex and new structural relationships within the genome.