CryptoDB:: a Cryptosporidium bioinformatics resource update

被引:118
作者
Heiges, Mark
Wang, Haiming
Robinson, Edward
Aurrecoechea, Cristina
Gao, Xin
Kaluskar, Nivedita
Rhodes, Philippa
Wang, Sammy
He, Cong-Zhou
Su, Yanqi
Miller, John
Kraemer, Eileen
Kissinger, Jessica C.
机构
[1] Univ Georgia, Ctr Trop & Emerging Global Dis, Dept Comp Sci, Athens, GA 30602 USA
[2] Univ Georgia, Dept Genet, Athens, GA 30602 USA
关键词
D O I
10.1093/nar/gkj078
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
The database, CryptoDB (http://CryptoDB.org), is a community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium. CryptoDB integrates whole genome sequence and annotation with expressed sequence tag and genome survey sequence data and provides supplemental bioinformatics analyses and data-mining tools. A simple, yet comprehensive web interface is available for mining and visualizing the data. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/ NIAID-fundedBioinformatics Resource Center. Recent updates to CryptoDB include the deposition of annotated genome sequences for Cryptosporidium parvum and Cryptosporidium hominis, migration to a relational database (GUS), a new query and visualization interface and the introduction of Web services.
引用
收藏
页码:D419 / D422
页数:4
相关论文
共 21 条
[1]   Complete genome sequence of the apicomplexan, Cryptosporidium parvum [J].
Abrahamsen, MS ;
Templeton, TJ ;
Enomoto, S ;
Abrahante, JE ;
Zhu, G ;
Lancto, CA ;
Deng, MQ ;
Liu, C ;
Widmer, G ;
Tzipori, S ;
Buck, GA ;
Xu, P ;
Bankier, AT ;
Dear, PH ;
Konfortov, BA ;
Spriggs, HF ;
Iyer, L ;
Anantharaman, V ;
Aravind, L ;
Kapur, V .
SCIENCE, 2004, 304 (5669) :441-445
[2]  
[Anonymous], 1997, CRYPTOSPORIDIUM CRYP
[3]   PlasmoDB:: the Plasmodium genome resource.: A database integrating experimental and computational data [J].
Bahl, A ;
Brunk, B ;
Crabtree, J ;
Fraunholz, MJ ;
Gajria, B ;
Grant, GR ;
Ginsburg, H ;
Gupta, D ;
Kissinger, JC ;
Labo, P ;
Li, L ;
Mailman, MD ;
Milgram, AJ ;
Pearson, DS ;
Roos, DS ;
Schug, J ;
Stoeckert, CJ ;
Whetzel, P .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :212-215
[4]   Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum [J].
Bankier, AT ;
Spriggs, HF ;
Fartmann, B ;
Konfortov, BA ;
Madera, M ;
Vogel, C ;
Teichmann, SA ;
Ivens, A ;
Dear, PH .
GENOME RESEARCH, 2003, 13 (08) :1787-1799
[5]   Improved prediction of signal peptides: SignalP 3.0 [J].
Bendtsen, JD ;
Nielsen, H ;
von Heijne, G ;
Brunak, S .
JOURNAL OF MOLECULAR BIOLOGY, 2004, 340 (04) :783-795
[6]   K2/Kleisli and GUS: Experiments in integrated access to genomic data sources [J].
Davidson, SB ;
Crabtree, J ;
Brunk, BP ;
Schug, J ;
Tannen, V ;
Overton, GC ;
Stoeckert, CJ .
IBM SYSTEMS JOURNAL, 2001, 40 (02) :512-531
[7]   The Distributed Annotation System [J].
Dowell, Robin D. ;
Jokerst, Rodney M. ;
Day, Allen ;
Eddy, Sean R. ;
Stein, Lincoln .
BMC BIOINFORMATICS, 2001, 2 (1)
[8]   PubCrawler: keeping up comfortably with PubMed and GenBank [J].
Hokamp, K ;
Wolfe, KH .
NUCLEIC ACIDS RESEARCH, 2004, 32 :W16-W19
[9]   ToxoDB:: accessing the Toxoplasma gondii genome [J].
Kissinger, JC ;
Gajria, B ;
Li, L ;
Paulsen, IT ;
Roos, DS .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :234-236
[10]   The Plasmodium genome database -: Designing and mining a eukaryotic genomics resource [J].
Kissinger, JC ;
Brunk, BP ;
Crabtree, J ;
Fraunholz, MJ ;
Gajria, B ;
Milgram, AJ ;
Pearson, DS ;
Schug, J ;
Bahl, A ;
Diskin, SJ ;
Ginsburg, H ;
Grant, GR ;
Gupta, D ;
Labo, P ;
Li, L ;
Mailman, MD ;
Mcweeney, SK ;
Whetzel, P ;
Stoeckert, CJ ;
Roos, DS .
NATURE, 2002, 419 (6906) :490-492