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Title

EuDBase: An online resource for automated EST analysis pipeline (ESTFrontier) and database for red seaweed Eucheuma denticulatum

 

Authors

Zeti Azura Mohamed Hussein11, 2*, Kok Keong Loke1, 2, Rabiatul Adawiah Zainal Abidin1, 2, Roohaida Othman1,3

 

Affiliation

1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia 43600 UKM Bangi, Selangor Malaysia; 2Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia; 3Centre for Gene Analysis and Technology, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia;

 

Email

zeti.amh@gmail.com; zzeti@ukm.my; *Corresponding author

 

Article Type

Database

 

Date

Received September 21, 2011; Accepted September 22, 2011; Published October 14, 2011

 

Abstract

Functional genomics has proven to be an efficient tool in identifying genes involved in various biological functions. However the availability of commercially important seaweed Eucheuma denticulatum functional resources is still limited. EuDBase is the first seaweed online repository that provides integrated access to ESTs of Eucheuma denticulatum generated from samples collected from Kudat and Semporna in Sabah, Malaysia. The database stored 10,031 ESTs that are clustered and assembled into 2,275 unique transcripts (UT) and 955 singletons. Raw data were automatically processed using ESTFrontier, an in-house automated EST analysis pipeline. Data was collected in MySQL database. Web interface is implemented using PHP and it allows browsing and querying EuDBase through search engine. Data is searchable via BLAST hit, domain search, Gene Ontology or KEGG Pathway. A user-friendly interface allows the identification of sequences either using a simple text query or similarity search. The development of EuDBase is initiated to store, manage and analyze the E. denticulatum ESTs and to provide accumulative digital resources for the use of global scientific community. EuDBase is freely available from http://www.inbiosis.ukm.my/eudbase/

 

Citation

Mohamed-Hussein et al. Bioinformation 7(4): 157-162 (2011)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.