PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae

<p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p< Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Palmeri Antonio [verfasserIn] Gherardini Pier Federico [verfasserIn] Tsigankov Polina [verfasserIn] Ausiello Gabriele [verfasserIn] Späth Gerald F [verfasserIn] Zilberstein Dan [verfasserIn] Helmer-Citterich Manuela [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2011

Übergeordnetes Werk:	In: BMC Genomics - BMC, 2003, 12(2011), 1, p 614
Übergeordnetes Werk:	volume:12 ; year:2011 ; number:1, p 614

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1471-2164-12-614

Katalog-ID:	DOAJ038460971

Internformat


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author_variant	p a pa g p f gpf t p tp a g ag s g f sgf z d zd h c m hcm
matchkey_str	article:14712164:2011----::hsrppopoyainierdcoseiifraaiipoooot
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allfields	10.1186/1471-2164-12-614 doi (DE-627)DOAJ038460971 (DE-599)DOAJ5359c17275264018abe6f05a04c695f6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Palmeri Antonio verfasserin aut PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p< Biotechnology Genetics Gherardini Pier Federico verfasserin aut Tsigankov Polina verfasserin aut Ausiello Gabriele verfasserin aut Späth Gerald F verfasserin aut Zilberstein Dan verfasserin aut Helmer-Citterich Manuela verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 614 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 614 https://doi.org/10.1186/1471-2164-12-614 kostenfrei https://doaj.org/article/5359c17275264018abe6f05a04c695f6 kostenfrei http://www.biomedcentral.com/1471-2164/12/614 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 614
spelling	10.1186/1471-2164-12-614 doi (DE-627)DOAJ038460971 (DE-599)DOAJ5359c17275264018abe6f05a04c695f6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Palmeri Antonio verfasserin aut PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p< Biotechnology Genetics Gherardini Pier Federico verfasserin aut Tsigankov Polina verfasserin aut Ausiello Gabriele verfasserin aut Späth Gerald F verfasserin aut Zilberstein Dan verfasserin aut Helmer-Citterich Manuela verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 614 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 614 https://doi.org/10.1186/1471-2164-12-614 kostenfrei https://doaj.org/article/5359c17275264018abe6f05a04c695f6 kostenfrei http://www.biomedcentral.com/1471-2164/12/614 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 614
allfields_unstemmed	10.1186/1471-2164-12-614 doi (DE-627)DOAJ038460971 (DE-599)DOAJ5359c17275264018abe6f05a04c695f6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Palmeri Antonio verfasserin aut PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p< Biotechnology Genetics Gherardini Pier Federico verfasserin aut Tsigankov Polina verfasserin aut Ausiello Gabriele verfasserin aut Späth Gerald F verfasserin aut Zilberstein Dan verfasserin aut Helmer-Citterich Manuela verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 614 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 614 https://doi.org/10.1186/1471-2164-12-614 kostenfrei https://doaj.org/article/5359c17275264018abe6f05a04c695f6 kostenfrei http://www.biomedcentral.com/1471-2164/12/614 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 614
allfieldsGer	10.1186/1471-2164-12-614 doi (DE-627)DOAJ038460971 (DE-599)DOAJ5359c17275264018abe6f05a04c695f6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Palmeri Antonio verfasserin aut PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p< Biotechnology Genetics Gherardini Pier Federico verfasserin aut Tsigankov Polina verfasserin aut Ausiello Gabriele verfasserin aut Späth Gerald F verfasserin aut Zilberstein Dan verfasserin aut Helmer-Citterich Manuela verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 614 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 614 https://doi.org/10.1186/1471-2164-12-614 kostenfrei https://doaj.org/article/5359c17275264018abe6f05a04c695f6 kostenfrei http://www.biomedcentral.com/1471-2164/12/614 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 614
allfieldsSound	10.1186/1471-2164-12-614 doi (DE-627)DOAJ038460971 (DE-599)DOAJ5359c17275264018abe6f05a04c695f6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Palmeri Antonio verfasserin aut PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p< Biotechnology Genetics Gherardini Pier Federico verfasserin aut Tsigankov Polina verfasserin aut Ausiello Gabriele verfasserin aut Späth Gerald F verfasserin aut Zilberstein Dan verfasserin aut Helmer-Citterich Manuela verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 614 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 614 https://doi.org/10.1186/1471-2164-12-614 kostenfrei https://doaj.org/article/5359c17275264018abe6f05a04c695f6 kostenfrei http://www.biomedcentral.com/1471-2164/12/614 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 614
language	English
source	In BMC Genomics 12(2011), 1, p 614 volume:12 year:2011 number:1, p 614
sourceStr	In BMC Genomics 12(2011), 1, p 614 volume:12 year:2011 number:1, p 614
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Biotechnology Genetics
isfreeaccess_bool	true
container_title	BMC Genomics
authorswithroles_txt_mv	Palmeri Antonio @@aut@@ Gherardini Pier Federico @@aut@@ Tsigankov Polina @@aut@@ Ausiello Gabriele @@aut@@ Späth Gerald F @@aut@@ Zilberstein Dan @@aut@@ Helmer-Citterich Manuela @@aut@@
publishDateDaySort_date	2011-01-01T00:00:00Z
hierarchy_top_id	326644954
id	DOAJ038460971
language_de	englisch
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Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. 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author	Palmeri Antonio
spellingShingle	Palmeri Antonio misc TP248.13-248.65 misc QH426-470 misc Biotechnology misc Genetics PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
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topic_title	TP248.13-248.65 QH426-470 PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
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title	PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
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title_full	PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
author_sort	Palmeri Antonio
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author_browse	Palmeri Antonio Gherardini Pier Federico Tsigankov Polina Ausiello Gabriele Späth Gerald F Zilberstein Dan Helmer-Citterich Manuela
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author-letter	Palmeri Antonio
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title_sort	phostryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
callnumber	TP248.13-248.65
title_auth	PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
abstract	<p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p<
abstractGer	<p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p<
abstract_unstemmed	<p<Abstract</p< <p<Background</p< <p<Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the <it<Leishmania </it<genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However <it<Leishmania </it<lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment.</p< <p<Results</p< <p<Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent <it<Leishmania </it<phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures <it<Leishmania</it<-specific phosphorylation features. More specifically our results show that <it<Leishmania </it<kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible <it<Leishmania</it<-specific phosphorylation motifs.</p< <p<We further demonstrate that this improvement in performance extends to the related trypanosomatids <it<Trypanosoma brucei </it<and <it<Trypanosoma cruzi</it<. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from <it<L. infantum, T. brucei and T. cruzi</it<.</p< <p<Conclusions</p< <p<Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at <url<http://phostryp.bio.uniroma2.it</url<</p<
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title_short	PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
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PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae

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