Abstract
BackgroundDNA 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.ResultsOur 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.ConclusionThe 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.
Highlights
DNA sequences have become a primary source of information in biodiversity analysis
For each species with 3 or more individuals, this tool plots maximum Within Species Divergence (Max-WSD) against minimum Between Species Divergence (Min-BSD) [7]
We plan to have an application programming interface (API) for our tools, allowing other developers to integrate our analyses into their own tools
Summary
The current implementation of iBarcode.org (July 2008) includes a sequence upload and management suite and nine analysis and visualization tools. In addition to this table, a reduced dataset containing unique haplotypes is produced in FASTA format. Between- vs within-species variation graph DNA barcoding is based on a simple premise: genetic variation between species exceeds that of within species This tool allows the user to visualize this principle in a given barcode dataset. For each species with 3 or more individuals, this tool plots maximum Within Species Divergence (Max-WSD) against minimum Between Species Divergence (Min-BSD) [7] The input for this tool is a genetic distance matrix (text format) produced either internally (by calculating number of nucleotide differences between and within species) or by common sequence analysis programs such as Mega [16]. We plan to have an application programming interface (API) for our tools, allowing other developers to integrate our analyses into their own tools
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