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

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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%.

Original language	English
Title of host publication	Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9781728155746
DOIs	https://doi.org/10.1109/CLEI47609.2019.235080
State	Published - Sep 2019
Event	45th Latin American Computing Conference, CLEI 2019 - Panama City, Panama Duration: 30 Sep 2019 → 4 Oct 2019

Publication series

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

Conference

Conference	45th Latin American Computing Conference, CLEI 2019
Country/Territory	Panama
City	Panama City
Period	30/09/19 → 4/10/19

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

factorial experiment
genes,
Metabucket
Pseudomona aeruginosa,
similarity
w-shingling

Access to Document

10.1109/CLEI47609.2019.235080

Cite this

Cedeno-Femandez, J., & Torres-Rojas, F. J. (2019). Using w-shingling to group similar genes into metabuckets. In Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019 Article 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\%.",

keywords = "factorial experiment, genes,, Metabucket, Pseudomona aeruginosa,, similarity, w-shingling",

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",

year = "2019",

month = sep,

doi = "10.1109/CLEI47609.2019.235080",

language = "Ingl{\'e}s",

series = "Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

booktitle = "Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019",

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Cedeno-Femandez, J & Torres-Rojas, FJ 2019, Using w-shingling to group similar genes into metabuckets. in 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, Panama, 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).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

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

AU - Cedeno-Femandez, Jorge

AU - Torres-Rojas, Francisco J.

PY - 2019/9

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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

UR - https://www.scopus.com/pages/publications/85084766298

U2 - 10.1109/CLEI47609.2019.235080

DO - 10.1109/CLEI47609.2019.235080

M3 - Contribución a la conferencia

AN - SCOPUS:85084766298

T3 - Proceedings - 2019 45th Latin American Computing Conference, CLEI 2019

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

Abstract

Publication series

Conference

UN SDGs

Keywords

Access to Document

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