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. 2006 Jan 1;34(Database issue):D398-401.
doi: 10.1093/nar/gkj033.

ShiBASE: an integrated database for comparative genomics of Shigella

Jian Yang  1 , Lihong Chen, Jun Yu, Lilian Sun, Qi Jin
Affiliations

ShiBASE: an integrated database for comparative genomics of Shigella

Jian Yang et al. Nucleic Acids Res. .

Abstract

Among the major enteric bacterial pathogens, Shigella is found to display extreme genome diversity and dynamics, which imposes a challenge in comparative genomic studies. To facilitate further studies in this area, we have constructed an integrated online database, ShiBASE (http://www.mgc.ac.cn/ShiBASE/),which contains Shigella genomic sequences of four species and additional comparative genomic hybridization (CGH) data of 43 serotypes. ShiBASE offers online comparative analysis on DNA sequences, gene orders, metabolic pathways and virulence factors. In addition, ShiBASE has a newly developed online comparative visualization service, Shi-align, which enables the alignment of any query sequence with the reference genome sequences.

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Figures

Figure 1
Figure 1
Sequence-based comparison in ShiBASE. (A) Shigella genome comparison view. Genome sequence of Sb227 was set as reference on the top. The current comparison window size is 20 kb and it can be increased by clicking the circular plus (‘+’) icon on the top left. Note that the reverse complementary strand of Sf301 was used in this comparison figure. Arrows represent genes, of which those with write cross or with dashed lines that connect separate portions are pseudogenes owing to mutations or insertions, respectively. The compared region contains a set of flagellar genes (fli) and they were inactivated by different pseudogenes in all four genomes. The left part of the corresponding region in Ss046 (on the bottom) was translocated elsewhere. (B) Result of Shi-align by querying with a ∼17 kb segment from EHEC. Coloured bars between each pair represent MSPs from BLASTN of different identity values: red, >95%; pink, 90–95%; and orange, <90%.
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