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OmniMapFree: A unified tool to visualise and explore sequenced genomes
• BACKGROUND: Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species,...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251307/ https://www.ncbi.nlm.nih.gov/pubmed/22085540 http://dx.doi.org/10.1186/1471-2105-12-447 |
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author | Antoniw, John Beacham, Andrew M Baldwin, Thomas K Urban, Martin Rudd, Jason J Hammond-Kosack, Kim E |
author_facet | Antoniw, John Beacham, Andrew M Baldwin, Thomas K Urban, Martin Rudd, Jason J Hammond-Kosack, Kim E |
author_sort | Antoniw, John |
collection | PubMed |
description | • BACKGROUND: Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome. • RESULTS: We have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality. • CONCLUSIONS: OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism. |
format | Online Article Text |
id | pubmed-3251307 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-32513072012-01-05 OmniMapFree: A unified tool to visualise and explore sequenced genomes Antoniw, John Beacham, Andrew M Baldwin, Thomas K Urban, Martin Rudd, Jason J Hammond-Kosack, Kim E BMC Bioinformatics Software • BACKGROUND: Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome. • RESULTS: We have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality. • CONCLUSIONS: OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism. BioMed Central 2011-11-15 /pmc/articles/PMC3251307/ /pubmed/22085540 http://dx.doi.org/10.1186/1471-2105-12-447 Text en Copyright © 2011 Antoniw et al; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Antoniw, John Beacham, Andrew M Baldwin, Thomas K Urban, Martin Rudd, Jason J Hammond-Kosack, Kim E OmniMapFree: A unified tool to visualise and explore sequenced genomes |
title | OmniMapFree: A unified tool to visualise and explore sequenced genomes |
title_full | OmniMapFree: A unified tool to visualise and explore sequenced genomes |
title_fullStr | OmniMapFree: A unified tool to visualise and explore sequenced genomes |
title_full_unstemmed | OmniMapFree: A unified tool to visualise and explore sequenced genomes |
title_short | OmniMapFree: A unified tool to visualise and explore sequenced genomes |
title_sort | omnimapfree: a unified tool to visualise and explore sequenced genomes |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251307/ https://www.ncbi.nlm.nih.gov/pubmed/22085540 http://dx.doi.org/10.1186/1471-2105-12-447 |
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