Using w-shingling to group similar genes into metabuckets

Jorge Cedeno-Femandez; Francisco J. Torres-Rojas

doi:10.1109/CLEI47609.2019.235080

Using w-shingling to group similar genes into metabuckets

Jorge Cedeno-Femandez
, Francisco J. Torres-Rojas

Costa Rica Institute of Technology

Producción científica: Capítulo del libro/informe/acta de congreso › Contribución a la conferencia › revisión exhaustiva

Resumen

The Pseudomonas aeruginosa AGI is an opportunistic superbug that affects patients with weakened immune systems due to infectious diseases in eyes, ears, burns or chronic diseases such as cystic flbrosis. This bacterium has genes without information and it is necessary to determine the function they fulfill in order to seek medical treatment that helps infected patients. Using w-shingling, metabuckets are generated that group genes by their similarity. Each metabucket contains genes with or without information, the latter can be associated with information about what they do possess. In addition, a factorial experiment is presented with the results of applying the algorithm to a set of genes obtained from public databases, where the average similarity of the genes grouped in metabuckets reaches 98%.

Idioma original	Inglés
Título de la publicación alojada	Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019
Editorial	Institute of Electrical and Electronics Engineers Inc.
ISBN (versión digital)	9781728155746
DOI	https://doi.org/10.1109/CLEI47609.2019.235080
Estado	Publicada - sept 2019
Evento	45th Latin American Computing Conference, CLEI 2019 - Panama City, Panamá Duración: 30 sept 2019 → 4 oct 2019

Serie de la publicación

Nombre	Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019

Conferencia

Conferencia	45th Latin American Computing Conference, CLEI 2019
País/Territorio	Panamá
Ciudad	Panama City
Período	30/09/19 → 4/10/19

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Cedeno-Femandez, J., & Torres-Rojas, F. J. (2019). Using w-shingling to group similar genes into metabuckets. En Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019 Artículo 9073862 (Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CLEI47609.2019.235080

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title = "Using w-shingling to group similar genes into metabuckets",

abstract = "The Pseudomonas aeruginosa AGI is an opportunistic superbug that affects patients with weakened immune systems due to infectious diseases in eyes, ears, burns or chronic diseases such as cystic flbrosis. This bacterium has genes without information and it is necessary to determine the function they fulfill in order to seek medical treatment that helps infected patients. Using w-shingling, metabuckets are generated that group genes by their similarity. Each metabucket contains genes with or without information, the latter can be associated with information about what they do possess. In addition, a factorial experiment is presented with the results of applying the algorithm to a set of genes obtained from public databases, where the average similarity of the genes grouped in metabuckets reaches 98\%.",

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author = "Jorge Cedeno-Femandez and Torres-Rojas, \{Francisco J.\}",

note = "Publisher Copyright: {\textcopyright} 2019 IEEE.; 45th Latin American Computing Conference, CLEI 2019 ; Conference date: 30-09-2019 Through 04-10-2019",

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doi = "10.1109/CLEI47609.2019.235080",

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Cedeno-Femandez, J & Torres-Rojas, FJ 2019, Using w-shingling to group similar genes into metabuckets. En Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019., 9073862, Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019, Institute of Electrical and Electronics Engineers Inc., 45th Latin American Computing Conference, CLEI 2019, Panama City, Panamá, 30/09/19. https://doi.org/10.1109/CLEI47609.2019.235080

Using w-shingling to group similar genes into metabuckets. / Cedeno-Femandez, Jorge; Torres-Rojas, Francisco J.
Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019. Institute of Electrical and Electronics Engineers Inc., 2019. 9073862 (Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019).

Producción científica: Capítulo del libro/informe/acta de congreso › Contribución a la conferencia › revisión exhaustiva

TY - GEN

T1 - Using w-shingling to group similar genes into metabuckets

AU - Cedeno-Femandez, Jorge

AU - Torres-Rojas, Francisco J.

PY - 2019/9

Y1 - 2019/9

N2 - The Pseudomonas aeruginosa AGI is an opportunistic superbug that affects patients with weakened immune systems due to infectious diseases in eyes, ears, burns or chronic diseases such as cystic flbrosis. This bacterium has genes without information and it is necessary to determine the function they fulfill in order to seek medical treatment that helps infected patients. Using w-shingling, metabuckets are generated that group genes by their similarity. Each metabucket contains genes with or without information, the latter can be associated with information about what they do possess. In addition, a factorial experiment is presented with the results of applying the algorithm to a set of genes obtained from public databases, where the average similarity of the genes grouped in metabuckets reaches 98%.

AB - The Pseudomonas aeruginosa AGI is an opportunistic superbug that affects patients with weakened immune systems due to infectious diseases in eyes, ears, burns or chronic diseases such as cystic flbrosis. This bacterium has genes without information and it is necessary to determine the function they fulfill in order to seek medical treatment that helps infected patients. Using w-shingling, metabuckets are generated that group genes by their similarity. Each metabucket contains genes with or without information, the latter can be associated with information about what they do possess. In addition, a factorial experiment is presented with the results of applying the algorithm to a set of genes obtained from public databases, where the average similarity of the genes grouped in metabuckets reaches 98%.

KW - factorial experiment

KW - genes,

KW - Metabucket

KW - Pseudomona aeruginosa,

KW - similarity

KW - w-shingling

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DO - 10.1109/CLEI47609.2019.235080

M3 - Contribución a la conferencia

AN - SCOPUS:85084766298

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BT - Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 45th Latin American Computing Conference, CLEI 2019

Y2 - 30 September 2019 through 4 October 2019

ER -

Using w-shingling to group similar genes into metabuckets

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