iRecSpot-EF: Effective sequence based features for recombination hotspot prediction.
Identifieur interne : 000756 ( Main/Exploration ); précédent : 000755; suivant : 000757iRecSpot-EF: Effective sequence based features for recombination hotspot prediction.
Auteurs : Md Rafsan Jani [Bangladesh] ; Md Toha Khan Mozlish [Bangladesh] ; Sajid Ahmed [Bangladesh] ; Niger Sultana Tahniat [Bangladesh] ; Dewan Md Farid [Bangladesh] ; Swakkhar Shatabda [Bangladesh]Source :
- Computers in biology and medicine [ 1879-0534 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA.
- genetics : Recombination, Genetic.
- methods : Genomics, Sequence Analysis, DNA.
- Algorithms, Databases, Genetic, Internet, Software.
Abstract
In genetic evolution, meiotic recombination plays an important role. Recombination introduces genetic variations and is a vital source of biodiversity and appears as a driving force in evolutionary development. Local regions of chromosomes where recombination events tend to be concentrated are known as hotspots and regions with relatively low frequencies of recombination are called coldspots. Predicting hotspots and coldspots can enlighten structure of recombination and genome evolution. In this paper, we proposed a predictor, called iRecSpot-EF to predict recombination hot and cold spots. iRecSpot-EF uses a novel set of features extracted from the genome sequences. We introduce the frequency of (l,k,p)-mers in the sequence as features. Our proposed feature extraction method hinges solely upon the nucleotide sequences, thus being cost-effective and robust. After feature extraction, the most informative features are selected using AdaBoost algorithm. We have selected logistic regression as the classification algorithm. iRecSpot-EF was tested on a standard benchmark dataset using cross-fold validation. It achieved an accuracy of 95.14% and area under Receiver Operating Characteristic curve (auROC) of 0.985. The performance of iRecSpot-EF is significantly better than the state-of-the-art methods. iRecSpot-EF is readily available for use from http://iRecSpot.pythonanywhere.com/server. All relevant codes are available via open repository at: https://github.com/mrzResearchArena/iRecSpot.
DOI: 10.1016/j.compbiomed.2018.10.005
PubMed: 30336361
Affiliations:
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Electronic address: rafsanjani.muhammod@gmail.com.</nlm:affiliation><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Computer Science and Engineering, United International University, Madani Avenue, Satarkul, Badda, Dhaka, 1212</wicri:regionArea><wicri:noRegion>1212</wicri:noRegion></affiliation></author><author><name sortKey="Khan Mozlish, Md Toha" sort="Khan Mozlish, Md Toha" uniqKey="Khan Mozlish M" first="Md Toha" last="Khan Mozlish">Md Toha Khan Mozlish</name><affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science and Engineering, United International University, Madani Avenue, Satarkul, Badda, Dhaka, 1212, Bangladesh. Electronic address: mmozlish141089@bscse.uiu.ac.bd.</nlm:affiliation><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Computer Science and Engineering, United International University, Madani Avenue, Satarkul, Badda, Dhaka, 1212</wicri:regionArea><wicri:noRegion>1212</wicri:noRegion></affiliation></author><author><name sortKey="Ahmed, Sajid" sort="Ahmed, Sajid" uniqKey="Ahmed S" first="Sajid" last="Ahmed">Sajid Ahmed</name><affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science and Engineering, United International University, Madani Avenue, Satarkul, Badda, Dhaka, 1212, Bangladesh. 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Electronic address: swakkhar@cse.uiu.ac.bd.</nlm:affiliation><country xml:lang="fr">Bangladesh</country><wicri:regionArea>Department of Computer Science and Engineering, United International University, Madani Avenue, Satarkul, Badda, Dhaka, 1212</wicri:regionArea><wicri:noRegion>1212</wicri:noRegion></affiliation></author></analytic><series><title level="j">Computers in biology and medicine</title><idno type="eISSN">1879-0534</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>DNA (genetics)</term><term>Databases, Genetic</term><term>Genomics (methods)</term><term>Internet</term><term>Recombination, Genetic (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (génétique)</term><term>Algorithmes</term><term>Analyse de séquence d'ADN ()</term><term>Bases de données génétiques</term><term>Génomique ()</term><term>Internet</term><term>Logiciel</term><term>Recombinaison génétique (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Recombination, Genetic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>Recombinaison génétique</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Databases, Genetic</term><term>Internet</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Bases de données génétiques</term><term>Génomique</term><term>Internet</term><term>Logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In genetic evolution, meiotic recombination plays an important role. Recombination introduces genetic variations and is a vital source of biodiversity and appears as a driving force in evolutionary development. Local regions of chromosomes where recombination events tend to be concentrated are known as hotspots and regions with relatively low frequencies of recombination are called coldspots. Predicting hotspots and coldspots can enlighten structure of recombination and genome evolution. In this paper, we proposed a predictor, called iRecSpot-EF to predict recombination hot and cold spots. iRecSpot-EF uses a novel set of features extracted from the genome sequences. We introduce the frequency of (l,k,p)-mers in the sequence as features. Our proposed feature extraction method hinges solely upon the nucleotide sequences, thus being cost-effective and robust. After feature extraction, the most informative features are selected using AdaBoost algorithm. We have selected logistic regression as the classification algorithm. iRecSpot-EF was tested on a standard benchmark dataset using cross-fold validation. It achieved an accuracy of 95.14% and area under Receiver Operating Characteristic curve (auROC) of 0.985. The performance of iRecSpot-EF is significantly better than the state-of-the-art methods. iRecSpot-EF is readily available for use from http://iRecSpot.pythonanywhere.com/server. All relevant codes are available via open repository at: https://github.com/mrzResearchArena/iRecSpot.</div></front></TEI><affiliations><list><country><li>Bangladesh</li></country></list><tree><country name="Bangladesh"><noRegion><name sortKey="Jani, Md Rafsan" sort="Jani, Md Rafsan" uniqKey="Jani M" first="Md Rafsan" last="Jani">Md Rafsan Jani</name></noRegion><name sortKey="Ahmed, Sajid" sort="Ahmed, Sajid" uniqKey="Ahmed S" first="Sajid" last="Ahmed">Sajid Ahmed</name><name sortKey="Farid, Dewan Md" sort="Farid, Dewan Md" uniqKey="Farid D" first="Dewan Md" last="Farid">Dewan Md Farid</name><name sortKey="Khan Mozlish, Md Toha" sort="Khan Mozlish, Md Toha" uniqKey="Khan Mozlish M" first="Md Toha" last="Khan Mozlish">Md Toha Khan Mozlish</name><name sortKey="Shatabda, Swakkhar" sort="Shatabda, Swakkhar" uniqKey="Shatabda S" first="Swakkhar" last="Shatabda">Swakkhar Shatabda</name><name sortKey="Tahniat, Niger Sultana" sort="Tahniat, Niger Sultana" uniqKey="Tahniat N" first="Niger Sultana" last="Tahniat">Niger Sultana Tahniat</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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