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ClonorESTdb: a comprehensive database for Clonorchis sinensis EST sequences.

Dae-Won Kim, Won Gi Yoo, Sanghyun Lee

  • 1Division of Malaria and Parasitic Diseases, Centre for Immunology and Pathology, Korea National Institute of Health, Chungbuk 363-951, Republic of Korea. leewonja@gmail.com.

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This study introduces ClonorESTdb, a database of Clonorchis sinensis expressed sequence tags (ESTs) for parasite genomics. It provides functional annotations and expression profiles to aid in drug development and biological research for clonorchiasis.

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Area of Science:

  • Parasitology
  • Genomics
  • Bioinformatics

Background:

  • Clonorchiasis, caused by liver fluke, is a fatal disease linked to bile duct cancer.
  • Genomic approaches are crucial for understanding parasite biology and pathology.
  • Organized databases of expressed sequence tags (ESTs) are needed for functional genomics.

Purpose of the Study:

  • To develop and present the ClonorESTdb database, a comprehensive resource for Clonorchis sinensis functional genomics.
  • To consolidate and annotate expressed sequence tag (EST) data for Clonorchis sinensis.

Main Methods:

  • Collected and processed 55,736 Clonorchis sinensis EST sequences from three cDNA libraries.
  • Clustered sequences into 13,305 non-redundant assembled ESTs (clusters and singletons).
  • Annotated sequences using BLAST and HMM against NCBI NR, UniProt, KEGG, and InterProScan.

Main Results:

  • The ClonorESTdb database contains 13,305 assembled C. sinensis EST sequences.
  • Includes functional annotations, expression profiles, tandem repeats, and single nucleotide polymorphisms.
  • Provides tools for local BLAST search and text retrieval for data exploration.

Conclusions:

  • ClonorESTdb facilitates identification and comparison of expression signatures across different biological stages.
  • Supports ongoing research in parasite drug and vaccine development.
  • Serves as a valuable resource for Clonorchis sinensis biological research.