Open Access Highly Accessed Database

Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis

Nikki Traylor-Knowles1, Brian R Granger23, Tristan J Lubinski2, Jignesh R Parikh23, Sara Garamszegi3, Yu Xia345, Jarrod A Marto67, Les Kaufman2 and John R Finnerty23*

Author Affiliations

1 Department of Biology, Stanford University, Hopkins Marine Station, Ocean View Blvd., Pacific Grove, CA, 93950, USA

2 Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA

3 Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA

4 Department of Chemistry, Boston University, 24 Cummington Street, Boston, MA 02215, USA

5 Department of Biomedical Engineering, Boston University, 24 Cummington Street, Boston, MA 02215, USA

6 Department of Cancer Biology and Blais Proteomics Center, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA

7 Department of Biological Chemistry and Molecular Pharmacology, 44 Binney Street, Harvard Medical School, Boston, MA 02115, USA

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BMC Genomics 2011, 12:585  doi:10.1186/1471-2164-12-585

Published: 29 November 2011

Additional files

Additional file 1:

A diagram depicting all of PocilloporaBase's tables and entity relationships as well as definitions for all fields.

Format: PDF Size: 163KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

A frequency histogram of the lengths of the assembled contigs in nucleotides. The number of contigs was summed for every 100-nucleotide increment in length (e.g., 0-99 nt, 100-199 nt; etc.).

Format: PDF Size: 477KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

A compressed text file containing all 70, 786 contigs reported in the manuscript.

Format: ZIP Size: 18.3MB Download file

Open Data

Additional file 4:

A pie chart summarizing the taxonomic affinities of non-metazoan, non-fungal, eukaryotic hits returned by BLAST searches.

Format: PDF Size: 28KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

A pie chart summarizing the taxonomic affinities of top hits to sequences from Alveolates (including dinoflagellates) returned by BLAST searches.

Format: PDF Size: 343KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Blast results from using P. damicornis contigs to query NCBI for scleractinian sequences.

Format: PDF Size: 154KB Download file

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Open Data

Additional file 7:

A complete listing of Gene Ontology terms and BLAST matches for all sequences.

Format: CSV Size: 1.8MB Download file

Open Data

Additional file 8:

A diagram depicting KEGG pathway elements and whether they were found or not found among the P. damicornis contigs.

Format: PPT Size: 1.4MB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 9:

A compressed folder containing an interactive (iPath) version of Additional File 7, which shows the metabolic pathways present in P. damicornis as inferred by BLASTx matches to human or plant genes with known metabolic functions.

Format: ZIP Size: 846KB Download file

Open Data