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Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms

David J McKillen12*, Yian A Chen12, Chuming Chen1, Matthew J Jenny12, Harold F Trent12, Javier Robalino12, David C McLean1, Paul S Gross123, Robert W Chapman234, Gregory W Warr123 and Jonas S Almeida12

Author Affiliations

1 Medical University of South Carolina, Charleston, South Carolina, 29425, USA

2 Departments of Biochemistry, of Biostatistics, Bioinformatics and Epidemiology. The Marine Biomedicine & Environmental Sciences Center (MBES), 221 Ft Johnson Rd., Charleston, SC 29412, USA

3 The Marine Genomics Consortium, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, South Carolina 29412-9110, USA

4 South Carolina Department of Natural Resources, 331 Ft. Johnson Road, Charleston SC 29412 (SCDNR), USA

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BMC Genomics 2005, 6:34  doi:10.1186/1471-2164-6-34

Published: 10 March 2005

Abstract

Background

The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs) and gene expression microarray data for marine organisms. It provides a unique clearing-house for marine specific EST and microarray data and is currently available at http://www.marinegenomics.org webcite.

Description

The Marine Genomics pipeline automates the processing, maintenance, storage and analysis of EST and microarray data for an increasing number of marine species. It currently contains 19 species databases (over 46,000 EST sequences) that are maintained by registered users from local and remote locations in Europe and South America in addition to the USA. A collection of analysis tools are implemented. These include a pipeline upload tool for EST FASTA file, sequence trace file and microarray data, an annotative text search, automated sequence trimming, sequence quality control (QA/QC) editing, sequence BLAST capabilities and a tool for interactive submission to GenBank. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB.

Conclusion

The conglomeration of multiple marine organisms with integrated analysis tools enables users to focus on the comprehensive descriptions of transcriptomic responses to typical marine stresses. This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment.