Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms.
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.


METHODS
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.


CONCLUSIONS
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.
McKillen
David J
DJ
Medical University of South Carolina, Charleston, South Carolina 29425, USA. mckilldj@musc.edu
Chen
Yian A
YA
Chen
Chuming
C
Jenny
Matthew J
MJ
Trent
Harold F
HF
Robalino
Javier
J
McLean
David C
DC
Gross
Paul S
PS
Chapman
Robert W
RW
Warr
Gregory W
GW
Almeida
Jonas S
JS
D000818:Animals; D037421:Anthozoa / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D004289:Dolphins / Q000235:genetics; D020224:Expressed Sequence Tags; D005399:Fishes / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods*; D020407:Internet; D008974:Mollusca / Q000235:genetics; D009316:National Institutes of Health (U.S.); D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000378:metabolism; D013045:Species Specificity; D014158:Transcription, Genetic; D014481:United States
D012333:RNA, Messenger