Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models

Background: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secre...

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Autores Principales: Restrepo-Montoya, Daniel, Becerra, David, Carvajal Patino, Juan, Mongui, Alvaro, Niño, Luis F., Patarroyo, Manuel E., Patarroyo, Manuel A.
Formato: Artículo (Article)
Lenguaje:Inglés (English)
Publicado: Universidad del Rosario 2011
Materias:
Acceso en línea:http://repository.urosario.edu.co/handle/10336/8839
id ir-10336-8839
recordtype dspace
spelling ir-10336-88392019-09-19T12:37:54Z Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models Restrepo-Montoya, Daniel Becerra, David Carvajal Patino, Juan Mongui, Alvaro Niño, Luis F. Patarroyo, Manuel E. Patarroyo, Manuel A. Enfermedades APICOMPLEXAN PARASITES MALARIA PARASITES IN-SILICO SUBCELLULAR-LOCALIZATION TOXOPLASMA-GONDII AOTUS MONKEYS FALCIPARUM PREDICTION DATABASE PEPTIDES Malaria Toxoplasmosis Plasmodium Background: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secretion and/or involvement in invasion-related processes. A profile-based sequence method supported by hidden Markov models (HMMs) was then used to build classifiers to search for biologically-related proteins. The transcriptional profile of the P. vivax intra-erythrocyte developmental cycle was then screened using these classifiers. Results: A bioinformatics methodology for identifying potentially secreted P. vivax proteins was designed using sequence redundancy reduction and probabilistic profiles. This methodology led to identifying a set of 45 proteins that are potentially secreted during the P. vivax intra-erythrocyte development cycle and could be involved in cell invasion. Thirteen of the 45 proteins have already been described as vaccine candidates; there is experimental evidence of protein expression for 7 of the 32 remaining ones, while no previous studies of expression, function or immunology have been carried out for the additional 25. Conclusions: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches. Also, different adjustments such as sequence redundancy reduction using Pisces or Cd-Hit allowed data clustering based on rational reproducible measurements. This kind of approach for selecting proteins with specific functions is highly important for supporting large-scale analyses that could aid in the identification of genes encoding potential new target antigens for vaccine development and drug design. The present study has led to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria. 2011-10-03 2014-08-13T19:38:44Z info:eu-repo/semantics/article info:eu-repo/semantics/acceptedVersion ISSN:ISSN:1932-6203 http://repository.urosario.edu.co/handle/10336/8839 eng info:eu-repo/semantics/openAccess application/pdf Universidad del Rosario reponame:Repositorio Institucional EdocUR instname:Universidad del Rosario
institution EdocUR - Universidad del Rosario
collection DSpace
language Inglés (English)
topic Enfermedades
APICOMPLEXAN PARASITES
MALARIA PARASITES
IN-SILICO
SUBCELLULAR-LOCALIZATION
TOXOPLASMA-GONDII
AOTUS MONKEYS
FALCIPARUM
PREDICTION
DATABASE
PEPTIDES
Malaria
Toxoplasmosis
Plasmodium
spellingShingle Enfermedades
APICOMPLEXAN PARASITES
MALARIA PARASITES
IN-SILICO
SUBCELLULAR-LOCALIZATION
TOXOPLASMA-GONDII
AOTUS MONKEYS
FALCIPARUM
PREDICTION
DATABASE
PEPTIDES
Malaria
Toxoplasmosis
Plasmodium
Restrepo-Montoya, Daniel
Becerra, David
Carvajal Patino, Juan
Mongui, Alvaro
Niño, Luis F.
Patarroyo, Manuel E.
Patarroyo, Manuel A.
Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models
description Background: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secretion and/or involvement in invasion-related processes. A profile-based sequence method supported by hidden Markov models (HMMs) was then used to build classifiers to search for biologically-related proteins. The transcriptional profile of the P. vivax intra-erythrocyte developmental cycle was then screened using these classifiers. Results: A bioinformatics methodology for identifying potentially secreted P. vivax proteins was designed using sequence redundancy reduction and probabilistic profiles. This methodology led to identifying a set of 45 proteins that are potentially secreted during the P. vivax intra-erythrocyte development cycle and could be involved in cell invasion. Thirteen of the 45 proteins have already been described as vaccine candidates; there is experimental evidence of protein expression for 7 of the 32 remaining ones, while no previous studies of expression, function or immunology have been carried out for the additional 25. Conclusions: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches. Also, different adjustments such as sequence redundancy reduction using Pisces or Cd-Hit allowed data clustering based on rational reproducible measurements. This kind of approach for selecting proteins with specific functions is highly important for supporting large-scale analyses that could aid in the identification of genes encoding potential new target antigens for vaccine development and drug design. The present study has led to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria.
format Artículo (Article)
author Restrepo-Montoya, Daniel
Becerra, David
Carvajal Patino, Juan
Mongui, Alvaro
Niño, Luis F.
Patarroyo, Manuel E.
Patarroyo, Manuel A.
author_facet Restrepo-Montoya, Daniel
Becerra, David
Carvajal Patino, Juan
Mongui, Alvaro
Niño, Luis F.
Patarroyo, Manuel E.
Patarroyo, Manuel A.
author_sort Restrepo-Montoya, Daniel
title Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models
title_short Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models
title_full Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models
title_fullStr Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models
title_full_unstemmed Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models
title_sort identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models
publisher Universidad del Rosario
publishDate 2011
url http://repository.urosario.edu.co/handle/10336/8839
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score 10,844952