Welcome to Dr. Zompo, the EST Repository for Seagrasses
Dr. Zompo was the first interactive seagrass sequence database,
initially containing a total of 4,606 expressed sequence tag (EST)
unigenes from two different seagrass species.
In the second version, more ESTs including next-generation
sequencing data have been added, increasing the total count to
> 95,000 tentative unigenes
for 2 seagrass species.
The main goal of this interactive database is to provide experimentalists with an easy access to the huge amount of sequences and their annotation in order to facilitate building experiments and considering challenges associated with the investigation of this class of non-domesticated monocotyledon systems.
Our database is based on the Ruby on Rails framework and is rich
in features including the retrieval of experimentally determined
heat-responsive transcripts and mining for molecular markers (SSRs and SNPs)
for some datasets. Weighted key word searches was also included
facilitating access to annotation gathered on several levels including
Pfam domains, GeneOntology and KEGG pathways.
Well established plant genome websites such as The Arabidopsis Information Resource (TAIR) and the Rice Genome Annotation Project are interfaced by Dr. Zompo. With this project, we have initialized a rich growing resource for plant biologists and the seagrass community to include the transcriptome of this non-model organism in their research efforts.
Wissler L, Dattolo E, Moore AD, Reusch TBH, Olsen JL, Migliaccio M, Bornberg-Bauer E, and Procaccini G
Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs
Database 2009; doi: 10.1093/database/bap009
Wissler L, Codoner FC, Gu J, Reusch TBH, Olsen JL, Procaccini G, and Bornberg-Bauer E
Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life
BMC Evolutionary Biology, 2011, 11:8
Reusch TBH, Veron AS, Preuss C, Weiner J, Wissler L, Beck A, Klages S, Kube M, Reinhardt R and Bornberg-Bauer E
Comparative Analysis of Expressed Sequence Tag (EST) Libraries in the Seagrass Zostera marina Subjected to Temperature Stress.
Mar Biotechnol, 2008, 10, 297-309
Details on Zoma_A and Pooc_A datasets [v1.0]In the first version of Dr.Zompo, we provided a collection of EST sequences gathered from two different seagrass species, Posidonia oceanica and Zostera marina. 9412, and 5185 raw sequence reads were reduced to a set of 3387 and 1219 unigenes for Zostera and Posidonia, respectively. Some analyses and annotations are exclusive to this dataset and include:
ContactWe appreciate any kind of feedback. In particular, if you encounter errors, or find bugs or inconsistencies, please let us know.
Main developer: Lothar Wissler