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diArk – a resource for eukaryotic genome research

BACKGROUND: The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interest...

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Detalles Bibliográficos
Autores principales: Odronitz, Florian, Hellkamp, Marcel, Kollmar, Martin
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868023/
https://www.ncbi.nlm.nih.gov/pubmed/17439643
http://dx.doi.org/10.1186/1471-2164-8-103
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author Odronitz, Florian
Hellkamp, Marcel
Kollmar, Martin
author_facet Odronitz, Florian
Hellkamp, Marcel
Kollmar, Martin
author_sort Odronitz, Florian
collection PubMed
description BACKGROUND: The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interested in single gene analyses (from a phylogenetic, a structural biology or other perspective) it is therefore important to have up-to-date knowledge about the various resources providing primary data. DESCRIPTION: The database is built around 3 central tables: species, sequencing projects and publications. The species table contains commonly and alternatively used scientific names, common names and the complete taxonomic information. For projects the sequence type and links to species project web-sites and species homepages are stored. All publications are linked to projects. The web-interface provides comprehensive search modules with detailed options and three different views of the selected data. We have especially focused on developing an elaborate taxonomic tree search tool that allows the user to instantaneously identify e.g. the closest relative to the organism of interest. CONCLUSION: We have developed a database, called diArk, to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes. Currently, diArk provides information about 415 eukaryotes, 823 sequencing projects, and 248 publications.
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spelling pubmed-18680232007-05-12 diArk – a resource for eukaryotic genome research Odronitz, Florian Hellkamp, Marcel Kollmar, Martin BMC Genomics Database BACKGROUND: The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interested in single gene analyses (from a phylogenetic, a structural biology or other perspective) it is therefore important to have up-to-date knowledge about the various resources providing primary data. DESCRIPTION: The database is built around 3 central tables: species, sequencing projects and publications. The species table contains commonly and alternatively used scientific names, common names and the complete taxonomic information. For projects the sequence type and links to species project web-sites and species homepages are stored. All publications are linked to projects. The web-interface provides comprehensive search modules with detailed options and three different views of the selected data. We have especially focused on developing an elaborate taxonomic tree search tool that allows the user to instantaneously identify e.g. the closest relative to the organism of interest. CONCLUSION: We have developed a database, called diArk, to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes. Currently, diArk provides information about 415 eukaryotes, 823 sequencing projects, and 248 publications. BioMed Central 2007-04-17 /pmc/articles/PMC1868023/ /pubmed/17439643 http://dx.doi.org/10.1186/1471-2164-8-103 Text en Copyright © 2007 Odronitz et al; licensee BioMed Central Ltd. http://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) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Odronitz, Florian
Hellkamp, Marcel
Kollmar, Martin
diArk – a resource for eukaryotic genome research
title diArk – a resource for eukaryotic genome research
title_full diArk – a resource for eukaryotic genome research
title_fullStr diArk – a resource for eukaryotic genome research
title_full_unstemmed diArk – a resource for eukaryotic genome research
title_short diArk – a resource for eukaryotic genome research
title_sort diark – a resource for eukaryotic genome research
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868023/
https://www.ncbi.nlm.nih.gov/pubmed/17439643
http://dx.doi.org/10.1186/1471-2164-8-103
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