ChamatusBase the Chionodraco hamatus muscle transcriptome database

ChamatusBase illustrates the first Chionodraco hamatus skeletal muscle transcriptome obtained from the assembly of 318,440 Roche 454 reads into 23,968 good-quality contigs.
C. hamatus (Notothenioidei, Perciformes) is an Antarctic fish belonging to the family Channichthyidae (icefish), the only example of adult vertebrates lacking haemoglobin and functionally active erythrocytes. C. hamatus is endemic to the Southern Ocean and is one of the most stenothermal species on Earth. It evolved over the past 6 million years in the persistently cold and oxygen-rich Antarctic waters and acquired extreme adaptations to freezing temperatures.
The database is searchable by contig ID, keywords and BLAST.

Summary

318,440 reads were obtained by 454 FLX Titanium sequencing of a normalized cDNA library constructed from sekeletal muscle tissue of 4 C. hamatus individuals. Reads were assembled into 23,968 contigs, representing bona fide individual transcripts, longer than 100 nucleotides and with an average sequence quality higher than 30. The 48% of contigs were annotated by similarity with at least one known sequence in nr and nt databases.

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)
• BLAST results (BLASTX against nr and BLASTN against nt): description and alignments

Example contig: http://compgen.bio.unipd.it/chamatusbase/contig/chionodraco_hamatus_c2571/

The database is searchable by keywords or BLAST against contig sequences; massive and customized data retrieval is allowed by the query system.

ChamatusBase is an open project developed at the University of Padova as a joint effort of the Department of Biology (Computational Genomics Laboratory and Molecular Ecology Group) and of the Department of Comparative Biomedicine and Food Sciences.