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Bioinformatics Vol. 19 no. 5 2003
Pages 661-662
© 2003 Oxford University Press

Applications Note

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts

Stefano Toppo *, Nicola Cannata , Paolo Fontana , Chiara Romualdi , Paolo Laveder , Emanuela Bertocco , Gerolamo Lanfranchi and Giorgio Valle *

CRIBI, Università di Padova, via Ugo Bassi 58/B, Padova, 35131 Italy

Received on September 3, 2002 ; revised on November 11, 2002 ; accepted on November 22, 2002

Summary: TRAIT is a knowledgebase integrating information on transcripts with related data from genome, proteins, ortholog genes and diseases. It was initially built as a system to manage an EST-based gene discovery project on human skeletal muscle, which yielded over 4500 independent sequence clusters. Transcripts are annotated using automatic as well as manual procedures, linking known transcripts to public databases and unknown transcripts to tables of predicted features. Data are stored in a MySQL database. Complex queries are automatically built by means of a user-friendly web interface that allows the concurrent selection of many fields such as ontology, expression level, map position and protein domains. The results are parsed by the system and returned in a ranked order, in respect to the number of satisfied criteria.

Availability: http://muscle.cribi.unipd.it and http://muscle.cribi.unipd.it/features/querystrait.html

Contact: stefano{at}cribi.unipd.it; giorgio.valle{at}unipd.it

* To whom correspondence should be addressed.


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