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Bioinformatics Advance Access originally published online on January 29, 2004
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Bioinformatics 20(6) © Oxford University Press 2004; all rights reserved.

The Hera database and its use in the characterization of endoplasmic reticulum proteins

M. Scott 1,3, G. Lu 2, M. Hallett 1 and D. Y. Thomas 3,*

1 McGill Center for Bioinformatics, Duff Medical Building, McGill University, 3755 University Street, Montreal, Quebec, Canada H3A 2B4, 2 Center for Biotechnology and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA and 3 Biochemistry Department, Faculty of Medicine, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6

Received on September 11, 2003 ; accepted on October 16, 2003
Advance Access Publication January 29, 2004

Motivation: Information concerning endoplasmic reticulum (ER) proteins is widely dispersed and cannot be easily and rapidly processed by the biological community. We present a comprehensive database of human ER proteins, called Human ER Aperçu (Hera). The Hera database was constructed by exhaustively searching through public databases and the scientific literature for ER proteins.

Results: Hera was used for the analysis of characteristics common to all human ER proteins. Our results show that a high proportion of ER proteins (59%) have at least one transmembrane domain and display physical characteristics consistent with this observation. In addition, one-third of ER proteins contain known ER retrieval or retention signals and 70% of ER proteins contain a signal peptide or anchor. Finally, 85% of ER proteins contain at least one InterPro motif. The most abundant InterPro motifs in ER proteins represent many of the most well-characterized functions of the ER.

Availability: Hera is available at http://www.mcb.mcgill.ca/~hera.

Contact: david.thomas{at}mcgill.ca

* To whom correspondence should be addressed.


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