Open Access Highly Accessed Database

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

Kyongyong Jung12, Jongsun Park123, Jaeyoung Choi12, Bongsoo Park4, Seungill Kim15, Kyohun Ahn1, Jaehyuk Choi23, Doil Choi5, Seogchan Kang4 and Yong-Hwan Lee1236*

Author Affiliations

1 Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea

2 Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea

3 Center for Fungal Genetic Resource, Seoul National University, Seoul 151-921, Korea

4 Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA

5 Department of Plant Science, Seoul National University, Seoul 151-921, Korea

6 Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea

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BMC Genomics 2008, 9:586  doi:10.1186/1471-2164-9-586

Published: 4 December 2008

Abstract

Background

Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP) was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed.

Results

The Seoul National University Genome Browser (SNUGB) integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets) and 34 plant and animal (38 datasets) species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion.

Conclusion

The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/ webcite.