Welcome to ESTree, version VI

The ESTree Interuniversitary Centre:

ESTree is an Interuniversitary Centre of several research units in Italy devoted to the implementation of genomics and functional genomics in peach.
Detailed information about the Centre is available in this document (English, Italian).

The primary objectives of the Centre are:

the development of an extensive EST database for peach (ESTree DB);
the analysis of several biochemical pathways based on oligonucleotide microarrays derived from ESTs collection;
the SNP-mapping of ESTs on available molecular linkage maps.

The current members of the Centre are:
Fondazione Parco Tecnologico Padano, FPTP, Lodi
Centre for Bio-molecular Interdisciplinary Studies and Industrial applications, CISI, Milan
University of Padua, Department of Biology - CRIBI
University of Padua, Department of Environmental Agronomy and Crop Science (DAAPV)
Istituto Sperimentale per la frutticoltura, Roma
Istituto di Biologia e Biotecnologie Agrarie- Sez. Roma, CNR
Trisaia and Casaccia Research Centres
University of Milan, Di.Pro.Ve
Sant'Anna School of Advanced Studies
Dipartimento di Scienze Agrarie e Ambientali (DiSA)
Dipartimento di Colture Arboree, Università di Bologna

The ESTree DB:

ESTree DB is a collection of Prunus persica and Prunus amygdalus EST sequences.
Sequenced clones belong to twelve peach libraries and three almond libraries produced in nine different labs:

Peach:
Libraries S1, S2, S3, S4 and Skin: produced in Milan, Italy, Dr. Pozzi's lab.
Library PP_LEa and PP_LEc: produced in Clemson, SC, USA, Prof. Abbott's lab.
Library Pp-S4: produced in Padua, Italy, Prof. Tonutti's lab.
Library S3II: produced in Padua, Italy, Dr. Trainotti's lab.
Library Lf: produced in Kearneysville, WV, USA, Dr. Callahan's lab.
Library PP_YEa: produced in Rome, Italy, Dr. Quarta's lab.
Library UD_S4: produced in Udine, Italy, by Dr G. Cipriani and Dr M.T. Marrazzo.
Libraries PU1, PU2, PU3 and PU4: produced in Santiago, Chile, Dr. Silva’s lab.
Library BG: produced in London, Canada, Dr. Wang’s lab.
Libraries F30 and F80: produced in Bordeaux, France, Dr. Le Dantec’s lab.

Almond:
Library PA_EST: produced in Beijing, China, Dr. Jiang's lab.
Library PA_AC: produced in Cabrils, Barcelona, Spain, Drs. Graziano's and Arus'slab.
Library PA_PA: produced in Clemson, SC, USA, Prof. Abbott's lab.

Sequence names begin with the library-of-origin name.

The current status of the ESTree DB is available here

The previous releases of the ESTree DB are available here: ESTree_Sept2006 (version V), ESTree_Aug2005, ESTree_Feb2005, ESTree_Oct2004, ESTree_Mar2004.
An ESTree version that includes only the sequences produced by Dr. Pozzi's Lab is available here: ESTree quality
As contig assembly programs automatically assign contig numbers that are different for each program run there is no correspondence between contigs with the same number belonging to the old and the new ESTree releases. The old releases is maintained to allow old contigs retrieval.


What's new in the 6th release - May 2007


Please cite

• "Lazzari B, Caprera A, Vecchietti A, Stella A, Milanesi L, Pozzi C.
  ESTree db: a tool for peach functional genomics. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S16. PMID: 16351742"
• Lazzari B, Caprera A, Vecchietti A, Merelli I, Barale F, Milanesi L, Stella A, Pozzi C.
  Version VI of the ESTree db: an improved tool for peach transcriptome analysis. BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S9. PMID: 18387211

Dr. Barbara Lazzari and Dr. Andrea Caprera: database and software implementation
Dr. Alberto Vecchietti: cDNA library production and sequences management
Dr. Alessandra Stella and Dr. Luciano Milanesi: Bioinformatics
Dr. Carlo Pozzi: ESTree project manager

Acknowledgements:

The realization of this webDB is supported by
Parco Tecnologico Padano
"Functional Genomics" MIUR 449/97
"Bioinformatics" FIRB project
C.I.S.I. (Centre for Bio-molecular Interdisciplinary Studies and Industrial Applications)
CNR-ITB (Istituto Tecnologie Biomediche - C.N.R.)
We are grateful to Dr. D. Edwards and Dr. G. Baker for providing the AutoSNP program.
We are grateful to Dr. S. Di Nardo and Dr. I. Merelli for helping us in establishing the multi-processor mpiBLAST procedure.
We are grateful to Dr. Alberto Montironi for preparing the bin assignment program.
We are grateful to Dr. Massoud Malek for informatical help.

Contact us:

info.ESTree * tecnoparco.org

For spamming reasons the @ symbol has been substituted with *




Annotations last update: July 2008