Database Commons

a catalog of worldwide biological databases

Cryptosporidium has historically been a difficult organism to work with, and molecular genomic data for this important pathogen have typically lagged behind other prominent protist pathogens. CryptoDB ( http://cryptodb.org/ ) was launched in 2004 following the appearance of draft genome sequences for both C. parvum and C. hominis. CryptoDB merged with the EuPathDB Bioinformatics Resource Center family of databases ( https://eupathdb.org ) and has been maintained and updated regularly since its establishment. These resources are freely available, are web-based, and permit users to analyze their own sequence data in the context of reference genome sequences in our user workspaces. Advances in technology have greatly facilitated Cryptosporidium research in the last several years greatly enhancing and extending the data and types of data available for this genus. Currently, 13 genome sequences are available for 9 species of Cryptosporidium as well as the distantly related Gregarina niphandrodes and two free-living alveolate outgroups of the Apicomplexa, Chromera velia and Vitrella brassicaformis. Recent years have seen several new genome sequences for both existing and new Cryptosporidium species as well as transcriptomics, proteomics, SNP, and isolate population surveys. This chapter introduces the extensive data mining and visualization capabilities of the EuPathDB software platform and introduces the data types and tools that are currently available for Cryptosporidium. Key features are demonstrated with Cryptosporidium-relevant examples and explanations.

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.

CryptoDB (http://CryptoDB.org) represents a collaborative effort to locate all genome data for the apicomplexan parasite Cryptosporidium parvum in a single user-friendly database. CryptoDB currently houses the genomic sequence data for both the human type 1 H strain and the bovine type 2 IOWA strain in addition to all other available EST and GSS sequences obtained from public repositories. All data are available for data mining via BLAST, keyword searches of pre-computed BLASTX results and user-defined or PROSITE motif pattern searches. Release 1.0 of CryptoDB contains approximately 19 million bases of genome sequence for the H and IOWA strains and an additional approximately 24 million bases of GSS and EST sequence obtained from other sources. Open reading frames greater than 50 and 100 amino acids have been generated for all sequences and all data are available for bulk download. This database, like other apicomplexan parasite databases, has been built utilizing the PlasmoDB model.