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In the absence of a highly conserved targeting signal, even motif searches may not be able to provide a lead for the accurate prediction of protein localization for a compartment of interest. In order to approach difficult cases of that kind, we propose an alternative method that complements existing approaches by using a more targeted protein sequence model. Moreover, our method makes use of (weighted) measures for time series comparison. To demonstrate its performance, we use this method for predicting localization in special compartments of three different species, for which existing methods yield only sub-optimal results. As shown experimentally, our method is indeed capable of producing reliable predictions of sub-cellular localization for difficult cases, i.e. if training data is scarce and a potential protein targeting signal may not be well conserved.<\/jats:p>","DOI":"10.1142\/s0219720013500169","type":"journal-article","created":{"date-parts":[[2013,10,21]],"date-time":"2013-10-21T05:38:26Z","timestamp":1382333906000},"page":"1350016","source":"Crossref","is-referenced-by-count":3,"title":["PROTEIN SUB-CELLULAR LOCALIZATION PREDICTION FOR SPECIAL COMPARTMENTS VIA OPTIMIZED TIME SERIES DISTANCES"],"prefix":"10.1142","volume":"12","author":[{"given":"MARCO","family":"MERNBERGER","sequence":"first","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein Stra\u00dfe, Marburg 35032, Germany"}]},{"given":"DANIEL","family":"MOOG","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, University of Marburg, Karl-von-Frisch Stra\u00dfe 8, Marburg 35043, Germany"},{"name":"LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Hans-Meerwein Stra\u00dfe, Marburg 35032, Germany"}]},{"given":"SIMONE","family":"STORK","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, University of Marburg, Karl-von-Frisch Stra\u00dfe 8, Marburg 35043, Germany"}]},{"given":"STEFAN","family":"ZAUNER","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, University of Marburg, Karl-von-Frisch Stra\u00dfe 8, Marburg 35043, Germany"}]},{"given":"UWE G.","family":"MAIER","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, University of Marburg, Karl-von-Frisch Stra\u00dfe 8, Marburg 35043, Germany"},{"name":"LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Hans-Meerwein Stra\u00dfe, Marburg 35032, Germany"}]},{"given":"EYKE","family":"H\u00dcLLERMEIER","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein Stra\u00dfe, Marburg 35032, Germany"},{"name":"LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Hans-Meerwein Stra\u00dfe, Marburg 35032, Germany"}]}],"member":"219","published-online":{"date-parts":[[2014,1,28]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1110\/ps.0303703"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2004.05.028"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.3903"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-6-152"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti309"},{"key":"rf6","first-page":"12","volume":"8","author":"Su E.","journal-title":"BMC Bioinformatics"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm259"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh350"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.2.298"},{"key":"rf10","first-page":"416","volume":"5","author":"Mak M.","journal-title":"IEEE\/ACM Trans Comput. 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