RuphiBase the Manila Clam (Ruditapes philippinarum) transcriptome database

RuphiBase reports results the first transcriptome sequencing and annotation of the bivalve mollusc Ruditapes philippinarum (Manila clam). RuphiBase entries are centred on contig sequence and annotation. The database is searchable by contig ID, key words and BLAST.
Summary
Starting from 463,424 total sequences including:

• 457,717 454 reads from a normalized cDNA library constructed with a mixture of adult tissues;
• 2,866 Sanger ESTs form the library cited above;
• 2,790 Sanger ESTs from a second normalized cDNA library from whole larvae and adult gonads;
• 51 publicly available mRNA;

a total of 191,624 sequences were assembled into 32,606 contigs representing the R. philippinarum transcriptome.

The 30% of contigs (9,747) resulted to be similar to a known protein or transcript.
About 40% of contigs similar to known proteins were associated to functional information (GO terms), corresponding to the 21% of the whole transcriptome.
For each contig, an entry reports the following data sections:

• Contig information (ID, description and FASTA sequence)
• Assembly (reads, contigs plus reads)
• Gene Ontology (Molecular Function, Biological Process, Cellular Component)
• Protein (NCBI nr database) BLAST results (Descriptions and Alignments)

Example contig: http://compgen.bio.unipd.it/ruphibase/contig/ruditapes_c2/
The database is searchable by keywords or BLAST against contig sequences; massive and customized data retrival is allowed by the query system.

RuphiBase is a project developed by the Computational Genomics and the Comparative Genomics Laboratories, University of Padova in the frame of a collaboration involving:

• Department of Evolutionary Biology, University of Florence, Italy
• Max Planck Institute for Molecular Genetics, Berlin, Germany
• CCMAR/University of Algarve, Faro, Portugal
• Instituto de Acuicultura de Torre la Sal (IATS), Consejo Superior de Investigaciones Cientificas (CSIC), Castellon, Spain