iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components

Meiosis and recombination are the two opposite aspects that coexist in a DNA system. As a driving force for evolution by generating natural genetic variations, meiotic recombination plays a very important role in the formation of eggs and sperm. Interestingly, the recombination does not occur random...

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Main Authors: Wang-Ren Qiu, Xuan Xiao, Kuo-Chen Chou
Format: Article
Language:English
Published: MDPI AG 2014-01-01
Series:International Journal of Molecular Sciences
Subjects:
DNA
Online Access:http://www.mdpi.com/1422-0067/15/2/1746
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spelling doaj-e62a360b1a80447bbfdad8ba2243646f2020-11-24T21:17:56ZengMDPI AGInternational Journal of Molecular Sciences1422-00672014-01-011521746176610.3390/ijms15021746ijms15021746iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid ComponentsWang-Ren Qiu0Xuan Xiao1Kuo-Chen Chou2Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen 333046, ChinaComputer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen 333046, ChinaCenter of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi ArabiaMeiosis and recombination are the two opposite aspects that coexist in a DNA system. As a driving force for evolution by generating natural genetic variations, meiotic recombination plays a very important role in the formation of eggs and sperm. Interestingly, the recombination does not occur randomly across a genome, but with higher probability in some genomic regions called “hotspots”, while with lower probability in so-called “coldspots”. With the ever-increasing amount of genome sequence data in the postgenomic era, computational methods for effectively identifying the hotspots and coldspots have become urgent as they can timely provide us with useful insights into the mechanism of meiotic recombination and the process of genome evolution as well. To meet the need, we developed a new predictor called “iRSpot-TNCPseAAC”, in which a DNA sample was formulated by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample according to its genetic codes. The former was used to incorporate its local or short-rage sequence order information; while the latter, its global and long-range one. Compared with the best existing predictor in this area, iRSpot-TNCPseAAC achieved higher rates in accuracy, Mathew’s correlation coefficient, and sensitivity, indicating that the new predictor may become a useful tool for identifying the recombination hotspots and coldspots, or, at least, become a complementary tool to the existing methods. It has not escaped our notice that the aforementioned novel approach to incorporate the DNA sequence order information into a discrete model may also be used for many other genome analysis problems. The web-server for iRSpot-TNCPseAAC is available at http://www.jci-bioinfo.cn/iRSpot-TNCPseAAC. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to obtain their desired result without the need to follow the complicated mathematical equations.http://www.mdpi.com/1422-0067/15/2/1746genomeDNArecombination spotshotspotscoldspotstrinucleotide compositionpseudo amino acid compositionweb-serveriRSpot-TNCPseAAC
collection DOAJ
language English
format Article
sources DOAJ
author Wang-Ren Qiu
Xuan Xiao
Kuo-Chen Chou
spellingShingle Wang-Ren Qiu
Xuan Xiao
Kuo-Chen Chou
iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components
International Journal of Molecular Sciences
genome
DNA
recombination spots
hotspots
coldspots
trinucleotide composition
pseudo amino acid composition
web-server
iRSpot-TNCPseAAC
author_facet Wang-Ren Qiu
Xuan Xiao
Kuo-Chen Chou
author_sort Wang-Ren Qiu
title iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components
title_short iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components
title_full iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components
title_fullStr iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components
title_full_unstemmed iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components
title_sort irspot-tncpseaac: identify recombination spots with trinucleotide composition and pseudo amino acid components
publisher MDPI AG
series International Journal of Molecular Sciences
issn 1422-0067
publishDate 2014-01-01
description Meiosis and recombination are the two opposite aspects that coexist in a DNA system. As a driving force for evolution by generating natural genetic variations, meiotic recombination plays a very important role in the formation of eggs and sperm. Interestingly, the recombination does not occur randomly across a genome, but with higher probability in some genomic regions called “hotspots”, while with lower probability in so-called “coldspots”. With the ever-increasing amount of genome sequence data in the postgenomic era, computational methods for effectively identifying the hotspots and coldspots have become urgent as they can timely provide us with useful insights into the mechanism of meiotic recombination and the process of genome evolution as well. To meet the need, we developed a new predictor called “iRSpot-TNCPseAAC”, in which a DNA sample was formulated by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample according to its genetic codes. The former was used to incorporate its local or short-rage sequence order information; while the latter, its global and long-range one. Compared with the best existing predictor in this area, iRSpot-TNCPseAAC achieved higher rates in accuracy, Mathew’s correlation coefficient, and sensitivity, indicating that the new predictor may become a useful tool for identifying the recombination hotspots and coldspots, or, at least, become a complementary tool to the existing methods. It has not escaped our notice that the aforementioned novel approach to incorporate the DNA sequence order information into a discrete model may also be used for many other genome analysis problems. The web-server for iRSpot-TNCPseAAC is available at http://www.jci-bioinfo.cn/iRSpot-TNCPseAAC. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to obtain their desired result without the need to follow the complicated mathematical equations.
topic genome
DNA
recombination spots
hotspots
coldspots
trinucleotide composition
pseudo amino acid composition
web-server
iRSpot-TNCPseAAC
url http://www.mdpi.com/1422-0067/15/2/1746
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AT xuanxiao irspottncpseaacidentifyrecombinationspotswithtrinucleotidecompositionandpseudoaminoacidcomponents
AT kuochenchou irspottncpseaacidentifyrecombinationspotswithtrinucleotidecompositionandpseudoaminoacidcomponents
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