ShiBASE:: an integrated database for comparative genomics of Shigella

被引：18

作者：

Yang, Jian

Chen, Lihong

Yu, Jun

Sun, Lilian

Jin, Qi ^{[1
]}

机构：

[1] State Key Lab Mol Virol & Genet Engn, Beijing 100176, Peoples R China

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷

关键词：

D O I：

10.1093/nar/gkj033

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

收藏

页码：D398 / D401

页数：4

相关论文

共 23 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] MolliGen, a database dedicated to the comparative genomics of Mollicutes [J].

Barré, A ;

de Daruvar, A ;

Blanchard, A .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D307-D310

[3]

Benson Dennis A, 2005, Nucleic Acids Res, V33, pD34

[4] ColiBASE:: an online database for Escherichia coli, Shigella and Salmonella comparative genomics [J].

Chaudhuri, RR ;

Khan, AM ;

Pallen, MJ .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D296-D299

[5] Activation of the CDC42 effector N-WASP by the Shigella flexneri IcsA protein promotes actin nucleation by Arp2/3 complex and bacterial actin-based motility [J].

Egile, C ;

Loisel, TP ;

Laurent, V ;

Li, R ;

Pantaloni, D ;

Sansonetti, PJ ;

Carlier, MF .

JOURNAL OF CELL BIOLOGY, 1999, 146 (06) :1319-1332

[6] Shigella flexneri infection:: pathogenesis and vaccine development [J].

Jennison, AV ;

Verma, NK .

FEMS MICROBIOLOGY REVIEWS, 2004, 28 (01) :43-58

[7] Genome sequence of Shigella flexneri 2a:: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157 [J].

Jin, Q ;

Yuan, ZH ;

Xu, JG ;

Wang, Y ;

Shen, Y ;

Lu, WC ;

Wang, JH ;

Liu, H ;

Yang, J ;

Yang, F ;

Zhang, XB ;

Zhang, JY ;

Yang, GW ;

Wu, HT ;

Qu, D ;

Dong, J ;

Sun, LL ;

Xue, Y ;

Zhao, AL ;

Gao, YS ;

Zhu, JP ;

Kan, B ;

Ding, KY ;

Chen, SX ;

Cheng, HS ;

Yao, ZJ ;

He, BK ;

Chen, RS ;

Ma, DL ;

Qiang, BQ ;

Wen, YM ;

Hou, YD ;

Yu, J .

NUCLEIC ACIDS RESEARCH, 2002, 30 (20) :4432-4441

[8] The KEGG resource for deciphering the genome [J].

Kanehisa, M ;

Goto, S ;

Kawashima, S ;

Okuno, Y ;

Hattori, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D277-D280

[9]

Kotloff KL, 1999, B WORLD HEALTH ORGAN, V77, P651

[10] Black holes and bacterial pathogenicity:: A large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli [J].

Maurelli, AT ;

Fernández, RE ;

Bloch, CA ;

Rode, CK ;

Fasano, A .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (07) :3943-3948