EeelBase 2.0 the European eel (Anguilla anguilla) transcriptome database version 2
EeelBase 2.0 is new version of EeelBase. It is based on a completely new assembly obtained from 640,040 reads including both 454 and Sanger sequences (see Pujolar et al. BMC Genomics 2012, 13:507 for full dataset description). EeelBase entries are centred on contig sequence and annotation. The database is searchable by contig ID, key words and BLAST.Database entry description. For each contig, a gene-like entry reports the following data sections:
- Contig information (ID, description and FASTA sequence)
- Functional annotation (GO terms)
- BLAST results (BLASTX againnst nr and UniProt/SwissProt, BLASTN against nt)): Description and Alignments
- Putative miRNAs, linked to miRBase
The database is searchable by keywords or BLAST against contig sequences; massive and customized data retrival is allowed by the query system.
EeelBase is an open project developed by the Computational Genomics Laboratory and the Molecular Ecology Group of the University of Padova.
It is intended to be a public and expandable resource provided to the scientific community. It is the first acquirement of Anguilla Genomics Consortium (AGC). Current AGC partners are:
- University of Padova, Italy (Lorenzo Zane)
- Katholieke Universiteit Leuven, Belgium (Gregory Maes)
- University of Laval, Canada (Louis Bernatchez)
- Aarhus University Denmark (Michael M. Hansen)
- University of St Andrews Scotland, UK (Gordon Cramb)
- University of Algarve Portugal (Adelino V.M. Canario )
- University of Algarve Portugal (Mar Huertas)
Please cite: Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the criticaly endangered European eel. Alessandro Coppe, Jose Martin Pujolar, Gregory E Maes, Peter F Larsen, Michael M Hansen, Louis Bernatchez, Lorenzo Zane, Stefania Bortoluzzi BMC Genomics 2010, 11:635
NEW: The first Eeelbase specific microarray has been released and tested. It comprises about 15,000 annotated cDNAs and it has been used for gene expression profiling of individuals from high (river Tiber, Italy) and low pollution (lake Bolsena, Italy) environments, which were measured for 36 PCBs, several organochlorine pesticides and brominated flame retardants and nine metals.
Please cite: Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel. Jose Martin Pujolar, Ilaria AM Marino, Massimo Milan, Alessandro Coppe, Gregory E Maes, Fabrizio Capoccioni, Eleonora Ciccotti, Lieven Bervoets, Adrian Covaci, Claude Belpaire, Gordon Cramb, Tomaso Patarnello, Luca Bargelloni, Stefania Bortoluzzi and Lorenzo Zane. BMC Genomics 2012, 13:507