CryptoDB: a Cryptosporidium bioinformatics resource update

The database, CryptoDB (), 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.

[1]  Gregory A. Buck,et al.  The genome of Cryptosporidium hominis , 2004, Nature.

[2]  Ping Xu,et al.  Complete Genome Sequence of the Apicomplexan, Cryptosporidium parvum , 2004, Science.

[3]  Li Li,et al.  ToxoDB: accessing the Toxoplasma gondii genome , 2003, Nucleic Acids Res..

[4]  Sarah A Teichmann,et al.  Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. , 2003, Genome research.

[5]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[6]  Amit P. Sheth,et al.  Framework for Semantic Web Process Composition , 2003, Int. J. Electron. Commer..

[7]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[8]  S. Brunak,et al.  Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.

[9]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[10]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[11]  Karsten Hokamp,et al.  PubCrawler: keeping up comfortably with PubMed and GenBank , 2004, Nucleic Acids Res..

[12]  Val Tannen,et al.  K2/Kleisli and GUS: Experiments in integrated access to genomic data sources , 2001, IBM Syst. J..

[13]  Gregory A. Buck,et al.  Corrigendum: The genome of Cryptosporidium hominis , 2004, Nature.

[14]  Li Li,et al.  PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data , 2003, Nucleic Acids Res..

[15]  W B Strong,et al.  Preliminary profile of the Cryptosporidium parvum genome: an expressed sequence tag and genome survey sequence analysis. , 2000, Molecular and biochemical parasitology.

[16]  S. Enomoto,et al.  Cryptosporidium and cryptosporidiosis. , 2005, Advances in parasitology.

[17]  Amos Bairoch,et al.  PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors , 2002, Briefings Bioinform..

[18]  Peter D. Karp,et al.  The Pathway Tools software , 2002, ISMB.

[19]  Li Li,et al.  ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites , 2004, Nucleic Acids Res..

[20]  L. Stein.  Creating a bioinformatics nation , 2002, Nature.

[21]  J. Schug,et al.  The Plasmodium genome database , 2002, Nature.