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iBarcode.org: web-based molecular biodiversity analysis.

Singer GA, Hajibabaei M - BMC Bioinformatics (2009)

Bottom Line: Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, N1G 2W1, Canada. gacsinger@gmail.com

ABSTRACT

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 http://www.ibarcode.org, 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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Related in: MedlinePlus

Species/Barcode cloud graphs tool in iBarcode.org. A. cloud representation of number of individuals per species for a set of primate CO1-barcodes [10]. B. cloud representation of within species sequence variation for the same primate data set. In each case the font size shows the relative value for each species.
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Figure 4: Species/Barcode cloud graphs tool in iBarcode.org. A. cloud representation of number of individuals per species for a set of primate CO1-barcodes [10]. B. cloud representation of within species sequence variation for the same primate data set. In each case the font size shows the relative value for each species.

Mentions: This module takes the popular "word cloud" concept and applies it to number of individuals of each species within a given barcode dataset, producing a visually-appealing means of seeing the relative abundance of species within a dataset. These relative abundances are linearly scaled between font sizes of 50 and 200 points. This feature also provides cloud visualization for sequence divergence within species and haplotype diversity in each species. Each species represented in the cloud visualization output can be selected to create a new subset dataset for further analysis using other tools. Figure 4 provides an example of a barcode cloud for a set of species of primates.


iBarcode.org: web-based molecular biodiversity analysis.

Singer GA, Hajibabaei M - BMC Bioinformatics (2009)

Species/Barcode cloud graphs tool in iBarcode.org. A. cloud representation of number of individuals per species for a set of primate CO1-barcodes [10]. B. cloud representation of within species sequence variation for the same primate data set. In each case the font size shows the relative value for each species.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697637&req=5

Figure 4: Species/Barcode cloud graphs tool in iBarcode.org. A. cloud representation of number of individuals per species for a set of primate CO1-barcodes [10]. B. cloud representation of within species sequence variation for the same primate data set. In each case the font size shows the relative value for each species.
Mentions: This module takes the popular "word cloud" concept and applies it to number of individuals of each species within a given barcode dataset, producing a visually-appealing means of seeing the relative abundance of species within a dataset. These relative abundances are linearly scaled between font sizes of 50 and 200 points. This feature also provides cloud visualization for sequence divergence within species and haplotype diversity in each species. Each species represented in the cloud visualization output can be selected to create a new subset dataset for further analysis using other tools. Figure 4 provides an example of a barcode cloud for a set of species of primates.

Bottom Line: Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, N1G 2W1, Canada. gacsinger@gmail.com

ABSTRACT

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 http://www.ibarcode.org, 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.

Show MeSH
Related in: MedlinePlus