Eel transcriptome sequencing.

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http://compgen.bio.unipd.it/eeelbase/

EeelBase reports results of the first European eel transcriptome sequencing and analysis. EeelBase entries are centred on contig sequence and annotation. The database is searchable by contig ID, key words and BLAST.


Summary
310,079 reads obtained by 454 FLX Titanium sequencing of a normalized cDNA library of 18 glass eels were assembled in 19,631 contigs (at least 200 nucleotides long and with average sequence quality not less than 30), representing bona fide individual transcripts. The 36% of contigs are annotated by similarity with at least one known sequence in UniProt or nr database; About two thirds of annotated contigs are associated to GO terms functional information; Contig sequences are aligned "on the fly" by UCSC Blat to Zebrafish and Stickleback genomes.

Database entry description. For each contig, a gene-like entry reports the following data sections:
Contig information (ID, description and FASTA sequence)
Assembly (reads and ACE multiple alignment)
Functional annotation (GO terms)
Zebrafish genome match in the UCSC Genome Browser
Stickleback genome match in the UCSC Genome Browser
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 open project developed by the Computational Genomics Laboratory 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)
New data contributions are welcome.

Please cite:Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically 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