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Nucleic Acids Research Advance Access originally published online on November 20, 2008
Nucleic Acids Research 2009 37(Database issue):D274-D278; doi:10.1093/nar/gkn862
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Nucleic Acids Research, 2009, Vol. 37, Database issue D274-D278
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

The Transporter Classification Database: recent advances

Milton H. Saier, Jr1,*, Ming Ren Yen1, Keith Noto2, Dorjee G. Tamang1 and Charles Elkan2

1Division of Biological Sciences and 2Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093-0116, USA

*To whom correspondence should be addressed. Tel: +1 858 534 4084; Fax: +1 858 534 7108; Email: msaier{at}ucsd.edu

Received September 16, 2008. Revised October 14, 2008. Accepted October 16, 2008.

The Transporter Classification Database (TCDB), freely accessible at http://www.tcdb.org, is a relational database containing sequence, structural, functional and evolutionary information about transport systems from a variety of living organisms, based on the International Union of Biochemistry and Molecular Biology-approved transporter classification (TC) system. It is a curated repository for factual information compiled largely from published references. It uses a functional/phylogenetic system of classification, and currently encompasses about 5000 representative transporters and putative transporters in more than 500 families. We here describe novel software designed to support and extend the usefulness of TCDB. Our recent efforts render it more user friendly, incorporate machine learning to input novel data in a semiautomatic fashion, and allow analyses that are more accurate and less time consuming. The availability of these tools has resulted in recognition of distant phylogenetic relationships and tremendous expansion of the information available to TCDB users.


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