Thu, 21 Aug 2008 07:17:20 BST CiteULike: xingxu Juncker http://www.citeulike.org/user/xingxu/author/Juncker CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/xingxu/article/2609190 <i>Protein Sci, Vol. 12, No. 8. (1 August 2003), pp. 1652-1662.</i><br /><br />A method to predict lipoprotein signal peptides in Gram-negative Eubacteria, LipoP, has been developed. The hidden Markov model (HMM) was able to distinguish between lipoproteins (SPaseII-cleaved proteins), SPaseI-cleaved proteins, cytoplasmic proteins, and transmembrane proteins. This predictor was able to predict 96.8% of the lipoproteins correctly with only 0.3% false positives in a set of SPaseI-cleaved, cytoplasmic, and transmembrane proteins. The results obtained were significantly better than those of previously developed methods. Even though Gram-positive lipoprotein signal peptides differ from Gram-negatives, the HMM was able to identify 92.9% of the lipoproteins included in a Gram-positive test set. A genome search was carried out for 12 Gram-negative genomes and one Gram-positive genome. The results for Escherichia coli K12 were compared with new experimental data, and the predictions by the HMM agree well with the experimentally verified lipoproteins. A neural network-based predictor was developed for comparison, and it gave very similar results. LipoP is available as a Web server at www.cbs.dtu.dk/services/LipoP/. 10.1110/ps.0303703 Prediction of lipoprotein signal peptides in Gram-negative bacteria Agnieszka Juncker Hanni Willenbrock Gunnar von Heijne Soren Brunak Henrik Nielsen Anders Krogh doi:10.1110/ps.0303703 Protein Sci, Vol. 12, No. 8. (1 August 2003), pp. 1652-1662. 2008-03-28T19:06:24-00:00 2003 Protein Sci 12 8 1652 1662 bioinformatics microbiology signal_peptides