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Nucleic Acids Research 2006 34(Web Server issue):W99-W103; doi:10.1093/nar/gkl351
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information

Sunghoon Lee1, Byungwook Lee1, Insoo Jang1, Sangsoo Kim1,2,* and Jong Bhak1,*

1 National Genome Information Center, Korea Research Institute of Bioscience and Biotechnology 52 Ueun-dong, Yuseong-gu, Daejeon 305-333, Republic of Korea 2 Department of Bioinformatics, Soongsil University 1-1 Sangdo-dong, Dongjak-gu, Seoul 156-743, Republic of Korea

*To whom correspondence should be addressed. Tel: +82 42 879 8500; Fax: + 82 42 879 8519; Email: jong{at}kribb.re.kr

*Corresponcdence may also be addressed to Sangsoo Kim. Tel: +82 2 820 0457; Fax: +82 2 824 4383; Email: sskimb{at}ssu.ac.kr

Received February 14, 2006. Revised March 1, 2006. Accepted April 19, 2006.

The Localizome server predicts the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein and presents the result as an intuitive graphic representation. It utilizes hmmpfam to detect the presence of Pfam domains and a prediction algorithm, Phobius, to predict the TM helices. The results are combined and checked against the TM topology rules stored in a protein domain database called LocaloDom. LocaloDom is a curated database that contains TM topologies and TM helix numbers of known protein domains. It was constructed from Pfam domains combined with Swiss-Prot annotations and Phobius predictions. The Localizome server corrects the combined results of the user sequence to conform to the rules stored in LocaloDom. Compared with other programs, this server showed the highest accuracy for TM topology prediction: for soluble proteins, the accuracy and coverage were 99 and 75%, respectively, while for TM protein domain regions, they were 96 and 68%, respectively. With a graphical representation of TM topology and TM helix positions with the domain units, the Localizome server is a highly accurate and comprehensive information source for subcellular localization for soluble proteins as well as membrane proteins. The Localizome server can be found at http://localizome.org/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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