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CryptoDB: the Cryptosporidium genome resource.

Daniela Puiu1, Shinichiro Enomoto, Gregory A Buck

  • 1Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.

Nucleic Acids Research
|December 19, 2003
PubMed
Summary
This summary is machine-generated.

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CryptoDB is a new database that centralizes genome data for Cryptosporidium parvum, a parasite. This resource aids researchers in mining genomic and sequence data for the human and bovine strains.

Area of Science:

  • Parasitology
  • Bioinformatics
  • Genomics

Background:

  • Apicomplexan parasites, including Cryptosporidium parvum, require centralized genomic resources for effective research.
  • Existing data repositories are fragmented, hindering comprehensive analysis of parasite biology.

Purpose of the Study:

  • To establish CryptoDB, a unified, user-friendly database for Cryptosporidium parvum genome data.
  • To facilitate data mining and analysis of genomic sequences for research on this important parasite.

Main Methods:

  • Aggregating genome sequence data for human type 1 H strain and bovine type 2 IOWA strain.
  • Incorporating expressed sequence tag (EST) and genome survey sequence (GSS) data from public repositories.
  • Implementing data mining tools including BLAST, keyword searches, and motif pattern searches.

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Main Results:

  • CryptoDB Release 1.0 contains approximately 19 million bases of genome sequence for two C. parvum strains.
  • An additional 24 million bases of GSS and EST sequences are available.
  • Open reading frames (ORFs) >50 and >100 amino acids have been generated, with bulk download options.

Conclusions:

  • CryptoDB provides a comprehensive and accessible platform for Cryptosporidium parvum research.
  • The database, built on the PlasmoDB model, supports advanced data mining and analysis.
  • Centralized genomic data in CryptoDB will accelerate discoveries in apicomplexan parasite biology.