ClonorESTdb: a comprehensive database for Clonorchis sinensis EST sequences

BMC Research Notes

Jung-Won Ju¹  Won-Ja Lee¹  Shin-Hyeong Cho¹  Yu-Jung Kim¹  Myoung-Ro Lee¹  Sanghyun Lee¹  Won Gi Yoo¹  Dae-Won Kim¹ 

[1] Division of Malaria and Parasitic Diseases, Centre for Immunology and Pathology, Korea National Institute of Health, Chungbuk 363-951, Republic of Korea

关键词: Database;    Transcriptome;    Expressed sequence tags (ESTs);    Clonorchis sinensis;   

Others  :  1132400
DOI  :  10.1186/1756-0500-7-388

 received in 2014-03-13, accepted in 2014-06-19,  发布年份 2014

【 摘 要 】

Background

Clonorchiasis, which is primarily caused by liver fluke (Platyhelminthes), is a fatal infectious disease that is mainly associated with bile duct malignancy and the subsequent development of cholangiocarcinoma. Thus, a genomic approach now represents an important step to further our knowledge of biology and the pathology of these parasites. The results of expressed sequence tags (ESTs) sequencing need to be well organized into databases to provide an integrated set of tools and functional information.

Findings

Here, the ClonorESTdb database represents a collection of Clonorchis sinensis ESTs that is intended as a resource for parasite functional genomics. A total of 55,736 successful EST sequences, which are cleaned and clustered into non-redundant 13,305 C. sinensis assembled EST sequences (6,497 clusters and 6,808 singletons), were obtained from three in-house prepared cDNA libraries of C. sinensis at different developmental stages. The assembled consensus sequences were annotated using the BLAST algorithm or/and hmm against NCBI NR, UniProt, KEGG and InterProScan. The ClonorESTdb database provides functional annotation, their expression profiles, tandem repeats and putative single nucleotide polymorphisms with utility tools such as local BLAST search and text retrieval.

Conclusions

This resource enables the researcher to identify and compare expression signatures under different biological stages and promotes ongoing parasite drug and vaccine development and biological research.

Database URL:http://pathod.cdc.go.kr/clonorestdb/ webcite

【 授权许可】

   
2014 Kim et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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