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iBarcode.org: web-based molecular biodiversity analysis

BACKGROUND: DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generat...

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Detalles Bibliográficos
Autores principales: Singer, Gregory AC, Hajibabaei, Mehrdad
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697637/
https://www.ncbi.nlm.nih.gov/pubmed/19534739
http://dx.doi.org/10.1186/1471-2105-10-S6-S14
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author Singer, Gregory AC
Hajibabaei, Mehrdad
author_facet Singer, Gregory AC
Hajibabaei, Mehrdad
author_sort Singer, Gregory AC
collection PubMed
description BACKGROUND: DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generated by laboratories that have an expertise in DNA sequencing but not in bioinformatics data analysis. Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets. RESULTS: Our web-based tools, available at , allow the user to manage their barcode datasets, cull out non-unique sequences, identify haplotypes within a species, and examine the within- to between-species divergences. In addition, we provide a number of phylogenetics tools that will allow the user to manipulate phylogenetic trees generated by other popular programs. CONCLUSION: The use of a web-based portal for barcode analysis is convenient, especially since the WWW is inherently platform-neutral. Indeed, we have even taken care to ensure that our website is usable from handheld devices such as PDAs and smartphones. Although the current set of tools available at iBarcode.org were developed to meet our own analytic needs, we hope that feedback from users will spark the development of future tools. We also welcome user-built modules that can be incorporated into the iBarcode framework.
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spelling pubmed-26976372009-06-16 iBarcode.org: web-based molecular biodiversity analysis Singer, Gregory AC Hajibabaei, Mehrdad BMC Bioinformatics Proceedings BACKGROUND: DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generated by laboratories that have an expertise in DNA sequencing but not in bioinformatics data analysis. Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets. RESULTS: Our web-based tools, available at , allow the user to manage their barcode datasets, cull out non-unique sequences, identify haplotypes within a species, and examine the within- to between-species divergences. In addition, we provide a number of phylogenetics tools that will allow the user to manipulate phylogenetic trees generated by other popular programs. CONCLUSION: The use of a web-based portal for barcode analysis is convenient, especially since the WWW is inherently platform-neutral. Indeed, we have even taken care to ensure that our website is usable from handheld devices such as PDAs and smartphones. Although the current set of tools available at iBarcode.org were developed to meet our own analytic needs, we hope that feedback from users will spark the development of future tools. We also welcome user-built modules that can be incorporated into the iBarcode framework. BioMed Central 2009-06-16 /pmc/articles/PMC2697637/ /pubmed/19534739 http://dx.doi.org/10.1186/1471-2105-10-S6-S14 Text en Copyright © 2009 Singer and Hajibabaei; 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 Proceedings
Singer, Gregory AC
Hajibabaei, Mehrdad
iBarcode.org: web-based molecular biodiversity analysis
title iBarcode.org: web-based molecular biodiversity analysis
title_full iBarcode.org: web-based molecular biodiversity analysis
title_fullStr iBarcode.org: web-based molecular biodiversity analysis
title_full_unstemmed iBarcode.org: web-based molecular biodiversity analysis
title_short iBarcode.org: web-based molecular biodiversity analysis
title_sort ibarcode.org: web-based molecular biodiversity analysis
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697637/
https://www.ncbi.nlm.nih.gov/pubmed/19534739
http://dx.doi.org/10.1186/1471-2105-10-S6-S14
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