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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

Test of selection at different taxonomic levels. Bar graphs representing the ratio of non-synonymous to synonymous nucleotide substitutions (ω) within species, within genus, and between genera for two exemplar data sets of fish [4] and bats [20].
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Figure 3: Test of selection at different taxonomic levels. Bar graphs representing the ratio of non-synonymous to synonymous nucleotide substitutions (ω) within species, within genus, and between genera for two exemplar data sets of fish [4] and bats [20].

Mentions: This module uses the popular ratio of non-synonymous to synonymous substitutions (ω) [13] at various taxonomic levels. This ratio has been used for estimating the degrees of selective pressure in molecular biosystematics. The module uses the program yn00 from the PAML package [14,15] to calculate the ratio of non-synonymous to synonymous substitutions (ω) for all pairs within a set of aligned sequences. It then calculates the average and standard deviation of ω for all sequences pairs that belong to the same species, belong to the same genus, or belong to different genera. A final bar graph depicting these various values is then displayed (Figure 3).


iBarcode.org: web-based molecular biodiversity analysis.

Singer GA, Hajibabaei M - BMC Bioinformatics (2009)

Test of selection at different taxonomic levels. Bar graphs representing the ratio of non-synonymous to synonymous nucleotide substitutions (ω) within species, within genus, and between genera for two exemplar data sets of fish [4] and bats [20].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Test of selection at different taxonomic levels. Bar graphs representing the ratio of non-synonymous to synonymous nucleotide substitutions (ω) within species, within genus, and between genera for two exemplar data sets of fish [4] and bats [20].
Mentions: This module uses the popular ratio of non-synonymous to synonymous substitutions (ω) [13] at various taxonomic levels. This ratio has been used for estimating the degrees of selective pressure in molecular biosystematics. The module uses the program yn00 from the PAML package [14,15] to calculate the ratio of non-synonymous to synonymous substitutions (ω) for all pairs within a set of aligned sequences. It then calculates the average and standard deviation of ω for all sequences pairs that belong to the same species, belong to the same genus, or belong to different genera. A final bar graph depicting these various values is then displayed (Figure 3).

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