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The classical NLS contains specific patterns of basic residues and computational methods have been designed to predict the location of these motifs on proteins. The consensus sequences, or patterns, for the other import pathways are less well-understood.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this paper, we present an analysis of characterized NLSs in yeast, and find, despite the large number of nuclear import pathways, that NLSs seem to show similar patterns of amino acid residues. We test current prediction methods and observe a low true positive rate. We therefore suggest an approach using hidden Markov models (HMMs) to predict novel NLSs in proteins. We show that our method is able to consistently find 37% of the NLSs with a low false positive rate and that our method retains its true positive rate outside of the yeast data set used for the training parameters.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Our implementation of this model, NLStradamus, is made available at: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.moseslab.csb.utoronto.ca\/NLStradamus\/\" ext-link-type=\"uri\">http:\/\/www.moseslab.csb.utoronto.ca\/NLStradamus\/<\/jats:ext-link>\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-202","type":"journal-article","created":{"date-parts":[[2009,6,30]],"date-time":"2009-06-30T06:15:04Z","timestamp":1246342504000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":626,"title":["NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction"],"prefix":"10.1186","volume":"10","author":[{"given":"Alex N","family":"Nguyen Ba","sequence":"first","affiliation":[]},{"given":"Anastassia","family":"Pogoutse","sequence":"additional","affiliation":[]},{"given":"Nicholas","family":"Provart","sequence":"additional","affiliation":[]},{"given":"Alan M","family":"Moses","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,6,29]]},"reference":[{"issue":"8","key":"2932_CR1","doi-asserted-by":"publisher","first-page":"5101","DOI":"10.1074\/jbc.R600026200","volume":"282","author":"A Lange","year":"2007","unstructured":"Lange A, Mills RE, Lange CJ, Stewart M, Devine SE, Corbett AH: J Biol Chem. 2007, 282(8):5101\u20135. 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