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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

Barcode-HAPMAP. An HTML representation of nucleotide characters unique to each haplotype in a set of barcode sequences. The exemplar data is from 4 species of skipper butterflies [12].
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Figure 2: Barcode-HAPMAP. An HTML representation of nucleotide characters unique to each haplotype in a set of barcode sequences. The exemplar data is from 4 species of skipper butterflies [12].

Mentions: This data visualization module provides a graphical view of the nucleotide character variation in a barcode data set. It allows the user to quickly pinpoint nucleotide positions within the barcode sequence that account for barcode variation in a set of species. The tool takes a FASTA alignment of barcode sequences (or the alignment of unique haplotypes created in the Haplotype Analysis tool from a given barcode dataset) as input and highlights variable positions across the barcode sequence in an easy-to-read format. It also shows the nucleotide position for each variable site (counting from 5' to 3') as well as the codon positions they belong to. It is therefore important that the FASTA file of the barcode sequences is in the correct reading frame. This tool works best for focused character-based analysis of a limited number of taxa (i.e. in a species complex or when dealing with cryptic species) as a complement to distance-based methods such as Neighbour-joining analysis [11]. The HTML output format generated by this tool allows robust data transfer to other software packages such as MS-Excel. Figure 2 is an exemplar Barcode-HAPMAP of the unique haplotypes in a set of 4 species of skipper butterflies (Lepidoptera:Hesperiidae) [12].


iBarcode.org: web-based molecular biodiversity analysis.

Singer GA, Hajibabaei M - BMC Bioinformatics (2009)

Barcode-HAPMAP. An HTML representation of nucleotide characters unique to each haplotype in a set of barcode sequences. The exemplar data is from 4 species of skipper butterflies [12].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Barcode-HAPMAP. An HTML representation of nucleotide characters unique to each haplotype in a set of barcode sequences. The exemplar data is from 4 species of skipper butterflies [12].
Mentions: This data visualization module provides a graphical view of the nucleotide character variation in a barcode data set. It allows the user to quickly pinpoint nucleotide positions within the barcode sequence that account for barcode variation in a set of species. The tool takes a FASTA alignment of barcode sequences (or the alignment of unique haplotypes created in the Haplotype Analysis tool from a given barcode dataset) as input and highlights variable positions across the barcode sequence in an easy-to-read format. It also shows the nucleotide position for each variable site (counting from 5' to 3') as well as the codon positions they belong to. It is therefore important that the FASTA file of the barcode sequences is in the correct reading frame. This tool works best for focused character-based analysis of a limited number of taxa (i.e. in a species complex or when dealing with cryptic species) as a complement to distance-based methods such as Neighbour-joining analysis [11]. The HTML output format generated by this tool allows robust data transfer to other software packages such as MS-Excel. Figure 2 is an exemplar Barcode-HAPMAP of the unique haplotypes in a set of 4 species of skipper butterflies (Lepidoptera:Hesperiidae) [12].

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