Brassica ASTRA:: an integrated database for Brassica genomic research

被引：28

作者：

Love, CG

Robinson, AJ

Lim, GAC

Hopkins, CJ

Batley, J

Barker, G

Spangenberg, GC

Edwards, D ^{[1
]}

机构：

[1] La Trobe Univ, Ctr Plant Biotechnol, Victorian Bioinformat Consortium, Bundoora, Vic 3086, Australia

[2] Univ Bristol, Sch Biol Sci, Bristol BS8 1UG, Avon, England

来源：

NUCLEIC ACIDS RESEARCH | 2005年 / 33卷

关键词：

D O I：

10.1093/nar/gki036

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：

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

引用

页码：D656 / D659

页数：4

共 10 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2] Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP [J].

Barker, G ;

Batley, J ;

O'Sullivan, H ;

Edwards, KJ ;

Edwards, D .

BIOINFORMATICS, 2003, 19 (03) :421-422

[3]

Benson DA, 2003, NUCLEIC ACIDS RES, V31, P23, DOI 10.1093/nar/gkg057

[4] The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 [J].

Boeckmann, B ;

Bairoch, A ;

Apweiler, R ;

Blatter, MC ;

Estreicher, A ;

Gasteiger, E ;

Martin, MJ ;

Michoud, K ;

O'Donovan, C ;

Phan, I ;

Pilbout, S ;

Schneider, M .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :365-370

[5] The Gene Ontology (GO) database and informatics resource [J].

Harris, MA ;

Clark, J ;

Ireland, A ;

Lomax, J ;

Ashburner, M ;

Foulger, R ;

Eilbeck, K ;

Lewis, S ;

Marshall, B ;

Mungall, C ;

Richter, J ;

Rubin, GM ;

Blake, JA ;

Bult, C ;

Dolan, M ;

Drabkin, H ;

Eppig, JT ;

Hill, DP ;

Ni, L ;

Ringwald, M ;

Balakrishnan, R ;

Cherry, JM ;

Christie, KR ;

Costanzo, MC ;

Dwight, SS ;

Engel, S ;

Fisk, DG ;

Hirschman, JE ;

Hong, EL ;

Nash, RS ;

Sethuraman, A ;

Theesfeld, CL ;

Botstein, D ;

Dolinski, K ;

Feierbach, B ;

Berardini, T ;

Mundodi, S ;

Rhee, SY ;

Apweiler, R ;

Barrell, D ;

Camon, E ;

Dimmer, E ;

Lee, V ;

Chisholm, R ;

Gaudet, P ;

Kibbe, W ;

Kishore, R ;

Schwarz, EM ;

Sternberg, P ;

Gwinn, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D258-D261

[6]

JAMES N, 2004, PLANT AN GEN 12 C, P999

[7] Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].

Kaul, S ;

Koo, HL ;

Jenkins, J ;

Rizzo, M ;

Rooney, T ;

Tallon, LJ ;

Feldblyum, T ;

Nierman, W ;

Benito, MI ;

Lin, XY ;

Town, CD ;

Venter, JC ;

Fraser, CM ;

Tabata, S ;

Nakamura, Y ;

Kaneko, T ;

Sato, S ;

Asamizu, E ;

Kato, T ;

Kotani, H ;

Sasamoto, S ;

Ecker, JR ;

Theologis, A ;

Federspiel, NA ;

Palm, CJ ;

Osborne, BI ;

Shinn, P ;

Conway, AB ;

Vysotskaia, VS ;

Dewar, K ;

Conn, L ;

Lenz, CA ;

Kim, CJ ;

Hansen, NF ;

Liu, SX ;

Buehler, E ;

Altafi, H ;

Sakano, H ;

Dunn, P ;

Lam, B ;

Pham, PK ;

Chao, Q ;

Nguyen, M ;

Yu, GX ;

Chen, HM ;

Southwick, A ;

Lee, JM ;

Miranda, M ;

Toriumi, MJ ;

Davis, RW .

NATURE, 2000, 408 (6814) :796-815

[8] TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets [J].

Pertea, G ;

Huang, XQ ;

Liang, F ;

Antonescu, V ;

Sultana, R ;

Karamycheva, S ;

Lee, Y ;

White, J ;

Cheung, F ;

Parvizi, B ;

Tsai, J ;

Quackenbush, J .

BIOINFORMATICS, 2003, 19 (05) :651-652

[9] The Arabidopsis Information Resource (TAIR):: a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community [J].

Rhee, SY ;

Beavis, W ;

Berardini, TZ ;

Chen, GH ;

Dixon, D ;

Doyle, A ;

Garcia-Hernandez, M ;

Huala, E ;

Lander, G ;

Montoya, M ;

Miller, N ;

Mueller, LA ;

Mundodi, S ;

Reiser, L ;

Tacklind, J ;

Weems, DC ;

Wu, YH ;

Xu, I ;

Yoo, D ;

Yoon, J ;

Zhang, PF .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :224-228

[10] Simple sequence repeat marker loci discovery using SSR primer [J].

Robinson, AJ ;

Love, CG ;

Batley, J ;

Barker, G ;

Edwards, D .

BIOINFORMATICS, 2004, 20 (09) :1475-1476

← 1 →