Validating subcellular localization prediction tools with mycobacterial proteins |
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Authors: | Daniel Restrepo-Montoya Carolina Vizcaíno Luis F Niño Marisol Ocampo Manuel E Patarroyo Manuel A Patarroyo |
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Institution: | 1. Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No, 26-20, Bogotá, DC, Colombia 2. Intelligent Systems Research Laboratory (LISI), Universidad Nacional de Colombia, Carrera 45 No, 26-85, Bogotá, DC, Colombia 3. Research Group on Combinatorial Algorithms (ALGOS-UN), Universidad Nacional de Colombia, Carrera 45 No, 26-85, Bogotá, DC, Colombia 4. School of Medicine,Universidad del Rosario, Carrera 24 No, 63C-69, Bogotá, DC, Colombia 5. School of Medicine,Universidad Nacional de Colombia, Carrera 45 No, 26-85, Bogotá, DC, Colombia
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Abstract: | Background The computational prediction of mycobacterial proteins' subcellular localization is of key importance for proteome annotation
and for the identification of new drug targets and vaccine candidates. Several subcellular localization classifiers have been
developed over the past few years, which have comprised both general localization and feature-based classifiers. Here, we
have validated the ability of different bioinformatics approaches, through the use of SignalP 2.0, TatP 1.0, LipoP 1.0, Phobius,
PA-SUB 2.5, PSORTb v.2.0.4 and Gpos-PLoc, to predict secreted bacterial proteins. These computational tools were compared
in terms of sensitivity, specificity and Matthew's correlation coefficient (MCC) using a set of mycobacterial proteins having
less than 40% identity, none of which are included in the training data sets of the validated tools and whose subcellular
localization have been experimentally confirmed. These proteins belong to the TBpred training data set, a computational tool
specifically designed to predict mycobacterial proteins. |
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