RNA family classification using the conditional random fields model

RNA family classification is one of the neccesary tasks needed to characterize sequenced genomes. RNA families are defined by member sequences which perform the same function in different species. Such functions have a strong relationship with RNA secondary structures but not the primary sequence. T...

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Main Authors:	Sitthichoke Subpaiboonkit, Chinae Thammarongtham, Jeerayut Chaijaruwanich
Format:	Journal
Published:	2018
Subjects:	Biochemistry, Genetics and Molecular Biology Chemistry Materials Science Mathematics Physics and Astronomy
Online Access:	https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84856571106&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/51426
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Institution:	Chiang Mai University

id	th-cmuir.6653943832-51426
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spelling	th-cmuir.6653943832-514262018-09-04T06:14:46Z RNA family classification using the conditional random fields model Sitthichoke Subpaiboonkit Chinae Thammarongtham Jeerayut Chaijaruwanich Biochemistry, Genetics and Molecular Biology Chemistry Materials Science Mathematics Physics and Astronomy RNA family classification is one of the neccesary tasks needed to characterize sequenced genomes. RNA families are defined by member sequences which perform the same function in different species. Such functions have a strong relationship with RNA secondary structures but not the primary sequence. Thus RNA sequences alone are not sufficient to classify RNA families. Here, we focus on computational RNA family classification by exploring primary sequences with RNA secondary structures as the selected feature to classify the RNA family using the method of conditional random fields (CRFs). This model treats RNA classification as a sequence labeling problem. Our CRFs models can classify the RNA families of the test RNA data sets with optimal F-score prediction between 98.77% - 99.32% for different RNA families. 2018-09-04T06:01:45Z 2018-09-04T06:01:45Z 2012-01-01 Journal 01252526 2-s2.0-84856571106 https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84856571106&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/51426
institution	Chiang Mai University
building	Chiang Mai University Library
country	Thailand
collection	CMU Intellectual Repository
topic	Biochemistry, Genetics and Molecular Biology Chemistry Materials Science Mathematics Physics and Astronomy
spellingShingle	Biochemistry, Genetics and Molecular Biology Chemistry Materials Science Mathematics Physics and Astronomy Sitthichoke Subpaiboonkit Chinae Thammarongtham Jeerayut Chaijaruwanich RNA family classification using the conditional random fields model
description	RNA family classification is one of the neccesary tasks needed to characterize sequenced genomes. RNA families are defined by member sequences which perform the same function in different species. Such functions have a strong relationship with RNA secondary structures but not the primary sequence. Thus RNA sequences alone are not sufficient to classify RNA families. Here, we focus on computational RNA family classification by exploring primary sequences with RNA secondary structures as the selected feature to classify the RNA family using the method of conditional random fields (CRFs). This model treats RNA classification as a sequence labeling problem. Our CRFs models can classify the RNA families of the test RNA data sets with optimal F-score prediction between 98.77% - 99.32% for different RNA families.
format	Journal
author	Sitthichoke Subpaiboonkit Chinae Thammarongtham Jeerayut Chaijaruwanich
author_facet	Sitthichoke Subpaiboonkit Chinae Thammarongtham Jeerayut Chaijaruwanich
author_sort	Sitthichoke Subpaiboonkit
title	RNA family classification using the conditional random fields model
title_short	RNA family classification using the conditional random fields model
title_full	RNA family classification using the conditional random fields model
title_fullStr	RNA family classification using the conditional random fields model
title_full_unstemmed	RNA family classification using the conditional random fields model
title_sort	rna family classification using the conditional random fields model
publishDate	2018
url	https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84856571106&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/51426
_version_	1681423767626055680

RNA family classification using the conditional random fields model

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