Marine Genomics: A Clearing house for genomic and transcriptomic data.

Welcome to the entry point of the Marine Genomics Project, Charleston South Carolina.

This is a web-based interface to bioinformatic data management and data analysis tools. The site has been developed by the bioinformatics group at the Hollings Marine Lab. as a part of the Medical University of South Carolina Charleston, SC. The Marine Genomics pipeline automates the processing, maintenance, storage and analysis for (currently) 121601 ESTs (Expressed Sequence Tags) or 16S RNA sequences and 1940 microarray experiments from 35 different marine species.

These species are maintained by registered users from local and remote locations in Europe and South America (in addition to the USA). A collection of EST and microarray analysis tools are implemented within Marine Genomics. 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, a microarray probe selection tool, an EST contig alignment tool, Gene Ontology listings, a tool for interactive submission to GenBank and more. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB which has enabled the development of microarray analysis tools which are now being implemented..

HOW TO USE THIS SITE

MARINE GENOMICS PUBLICATION

PIPELINE PROCESS FLOW CHART

ABOUT THE SCIENCE BEHIND MG (GENERAL DESCRIPTION)

PERSONAL SPECIES ACCOUNT CREATION (BECOME A CURATOR)
If you wish to take advantage of the MarineGenomics.org database please consider becoming a species curator and submitting your information to us.

BENEFITS:

EST AND 16S RNA SEQUENCE UPLOAD AND MANAGEMENT UTILITY
Curators can upload squence data to our local database servers where it will be automatically run through QA/QC. Browsing and curator assisted NCBI submissions are then made available.

SEQUENCE BLAST/ANNOTATION UTILITY
Sequence data is BLAST against the following databases:

- Entire MarineGenomics.org internal database collection
- NCBI NR
- NCBI NT
- NCBI dbest
- GO
- Individual species databases

SEQUENCE ANNOTATIVE SEARCH UTILITY
All MarineGenomics.org species data can be searched via the annotative search functions. Searches include all BLAST results, tissue, notes, filenames, MarineGenomics ID, NCBI accession numbers as well as GO molecular, biological and cellular function.

SEQUENCE CONTIG AND CLUSTER UTILITY
Once sequence data has been successfully upload to our databases, registered curators can review contig and cluster formations.

MICROARRAY UPLOAD AND MANAGEMENT UTILITY
Registered curators can browse, upload and manage microarray data. Currently MarineGenomics.org is accepting array data processed through in-house Hollings Marine Lab methods.

MICROARRAY ANALYSIS UTILITY
Registered curators can analyze their data using the following statistical functions made available to them:

- Array data easy retrieval to MATLAB
- Array 'bad-spot' filtering
- Within-array calibration
- Spearman/Pearson values
- Differential expression values determination
- Array clustering
- Excel report generation of all values including differential values, p-values, fold difference values between spots across arrays etc.
- graphical reports
- Principle component analysis

CURATOR PUBLICATION AND CONTACT LISTING
Registered curators can list both publications and contact information pertaining to Marine Genomics related research.

How to use this site: Both public and species-curators can browse all data within the Marine Genomics website. All species-specific data is accessible via the species links to the right of the page. Curators have permissions to curate and edit their species data, resume/CV information, publications they wish to make available on MG as well as addition/deletion of related projects that might have significance to the community. Curators wishing to edit their personal data can login in the upper right hand corner of the screen and subsequently click on the orange edit button that will appear at the top right hand corner. EST-data editing can be done directly within the species pages, once curators are logged in.

News and Articles :

HML Marine Genomics Reasearch connected to human health - Medical University Catalyst newspaper 05-26-05.

Algorithmically Speaking - Charleston City Paper 05-04-05

This work is was partially supported by the National Science Foundation (0315393, EPS0083102 & MCB0315393), the South Carolina Sea Grant Consortium (R/MT-6), and the South Carolina Department of Natural Resources. This is publication #20 from the Marine Biomedicine and Environmental Sciences at the Medical University of South Carolina. We also acknowledge the support by the South Carolina Sea Grant (NA16RG2250). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the supporting bodies mentioned herein.