KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

Handle URI:
http://hdl.handle.net/10754/552548
Title:
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
Authors:
Wang, Dapeng; Zhang, Yubin; Zhang, Zhang; Zhu, Jiang; Yu, Jun
Abstract:
We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5' to 3' direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.
KAUST Department:
Plant Stress Genomics Research Lab; Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies 2010, 8 (1):77 Genomics, Proteomics & Bioinformatics
Publisher:
Elsevier BV
Journal:
Genomics, Proteomics & Bioinformatics
Issue Date:
5-May-2010
DOI:
10.1016/S1672-0229(10)60008-3
Type:
Article
ISSN:
16720229
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S1672022910600083
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, Dapengen
dc.contributor.authorZhang, Yubinen
dc.contributor.authorZhang, Zhangen
dc.contributor.authorZhu, Jiangen
dc.contributor.authorYu, Junen
dc.date.accessioned2015-05-10T14:28:23Zen
dc.date.available2015-05-10T14:28:23Zen
dc.date.issued2010-05-05en
dc.identifier.citationKaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies 2010, 8 (1):77 Genomics, Proteomics & Bioinformaticsen
dc.identifier.issn16720229en
dc.identifier.doi10.1016/S1672-0229(10)60008-3en
dc.identifier.urihttp://hdl.handle.net/10754/552548en
dc.description.abstractWe present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5' to 3' direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.en
dc.publisherElsevier BVen
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S1672022910600083en
dc.rightsArchived with thanks to Genomics, Proteomics & Bioinformatics. http://creativecommons.org/licenses/by-nc-sa/3.0/en
dc.subjectKa/Ksen
dc.subjectgamma-series methodsen
dc.subjectsliding windowen
dc.subjectpositively selected sitesen
dc.titleKaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategiesen
dc.typeArticleen
dc.contributor.departmentPlant Stress Genomics Research Laben
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalGenomics, Proteomics & Bioinformaticsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, Chinaen
dc.contributor.institutionInstitute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, Chinaen
dc.contributor.institutionGraduate University of Chinese Academy of Sciences, Beijing 100049, Chinaen
kaust.authorZhang, Zhangen
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