[Coral-List] PocilloporaBase is now available!!

Nikki Traylor-Knowles ntk17 at bu.edu
Mon Dec 5 02:33:14 EST 2011

Dear Coral-List,

We at the Finnerty and Kaufman Labs of Boston University are excited to
announce the public release of PocilloporaBase, the *Pocillopora
damicornis*transcriptome database (www. PocilloporaBase.org ).  This
database houses
assembled contigs and raw reads sequenced at Agencourt using the 454
platform. Adult specimens for this project were gathered from various
Hawaiian populations and subjected to different stressors (including heat
shock, peroxide, hypo-salinity, and desiccation) as well as control
conditions. All of this RNA was pooled and sequenced using the 454
platform.  This was done in an effort to have a stress-enriched reference
transcriptome to assist future genomic and transcriptomic studies.
Functions available on PocilloporaBase include Blast, Kegg, Pfam, and GO
term searches. The assembled and raw reads may also be obtained. A
provisional manuscript describing bioinformatics analyses on these data and
the structure of the database is also available at:


In the coming months and years, PocilloporaBase will experience significant
growth as new transcriptomic and genomic datasets from ongoing *P.
damicornis* projects in the Finnerty and Kaufman labs are made available
there. Please contact us if you are interested in depositing your own
sequences at PocilloporaBase or if you have suggestions on the structure of
the database, the web interface, the output, or the search modalities

Nikki Traylor-Knowles performed collections, stress experiments, and RNA
isolations. Bob Richmond and Mark Martindale (U. Hawaii) provided critical
technical advice and logistical support for the fieldwork, laboratory
stress experiments, and RNA isolations. Brian Granger, Tristan Lubinski,
spear-headed the database construction and implementation with substantial
assistance from Jignesh Parikh (BU),Sara Garamszegi (BU), Yu Xia (BU), and
Jarrod A. Marto (Harvard).

This work was funded by Conservation International, as part of the Marine
Management Area Science and Climate Change programs.  PocilloporaBase is a
contribution to the “Coral Whisperer” project, a collaboration among six
institutions to employ coral holobiont transcriptomics as a differential
diagnostic for local and global environmental stressors.

The site is still under construction and will be periodically changing, so
if you have any problems or issues with accessing it, please contact us at
CnidTeam at gmail.com

We hope that you enjoy our site, and that this can be a help to you and
your research.

Coral Love,

Nikki Traylor-Knowles

Postdoctoral Scholar at Hopkins Marine Station, Stanford University


The Finnerty Lab and Kaufman Lab

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