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This article is part of the supplement: Eighth International Conference on Bioinformatics (InCoB2009): Computational Biology

Open Access Proceedings

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources

Jeongheui Lim1, Sang-Yoon Kim1, Sungmin Kim2, Hae-Seok Eo3, Chang-Bae Kim4, Woon Kee Paek5, Won Kim2* and Jong Bhak1*

Author Affiliations

1 Korean BioInformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea

2 School of Biological Science, Seoul National University, Seoul, 151-742, Korea

3 School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 130-722, Korea

4 Department of Life Science, Sangmyung University, Seoul, 110-743, Korea

5 Division of Natural History, National Science Museum, Daejeon, 305-705, Korea

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BMC Genomics 2009, 10(Suppl 3):S8  doi:10.1186/1471-2164-10-S3-S8

Published: 3 December 2009

Abstract

Background

DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases.

Results

We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses.

Conclusion

Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system http://www.asianbarcode.org webcite.