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Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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

Cited 17 times inthomson ciCited 23 times inthomson ci
Title
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
Other Titles
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
Author
Lee, SunghoonLee, ByungwookJang, InsooKim, SangsooBhak, Jong Hwa
Keywords
MEMBRANE-PROTEINS; PREDICTION SERVER; HUMAN GENOME; SEQUENCE; LOCALIZATION; DATABASE; MODEL
Issue Date
2006-07
Publisher
OXFORD UNIV PRESS
Citation
NUCLEIC ACIDS RESEARCH, v.34, no., pp.W99 - W103
Abstract
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/
URI
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DOI
10.1093/nar/gkl351
ISSN
0305-1048
Appears in Collections:
BME_Journal Papers
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