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Article: MBEToolbox: A Matlab toolbox for sequence data analysis in molecular biology and evolution

TitleMBEToolbox: A Matlab toolbox for sequence data analysis in molecular biology and evolution
Authors
Issue Date2005
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcbioinformatics/
Citation
Bmc Bioinformatics, 2005, v. 6 How to Cite?
AbstractBackground: MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results: We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion: MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/ project/?group_id=454. © 2005 Cai et al; licensee BioMed Central Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/53321
ISSN
2015 Impact Factor: 2.435
2015 SCImago Journal Rankings: 1.722
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorCai, JJen_HK
dc.contributor.authorSmith, DKen_HK
dc.contributor.authorXia, Xen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2009-04-03T07:12:19Z-
dc.date.available2009-04-03T07:12:19Z-
dc.date.issued2005en_HK
dc.identifier.citationBmc Bioinformatics, 2005, v. 6en_HK
dc.identifier.issn1471-2105en_HK
dc.identifier.urihttp://hdl.handle.net/10722/53321-
dc.description.abstractBackground: MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results: We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion: MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/ project/?group_id=454. © 2005 Cai et al; licensee BioMed Central Ltd.en_HK
dc.languageengen_HK
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcbioinformatics/en_HK
dc.relation.ispartofBMC Bioinformaticsen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsB M C Bioinformatics. Copyright © BioMed Central Ltd.en_HK
dc.subject.meshComputational Biology - methodsen_HK
dc.subject.meshMolecular Biology - methodsen_HK
dc.subject.meshDatabase Management Systemsen_HK
dc.subject.meshOligonucleotide Array Sequence Analysisen_HK
dc.subject.meshSignal Processing, Computer-Assisteden_HK
dc.titleMBEToolbox: A Matlab toolbox for sequence data analysis in molecular biology and evolutionen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2105&volume=6&issue=1&spage=64&epage=&date=2005&atitle=MBEToolbox:+a+MATLAB+toolbox+for+sequence+data+analysis+in+molecular+biology+and+evolutionen_HK
dc.identifier.emailYuen, KY:kyyuen@hkucc.hku.hken_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1186/1471-2105-6-64en_HK
dc.identifier.pmid15780146en_HK
dc.identifier.pmcidPMC1274259-
dc.identifier.scopuseid_2-s2.0-22344451035en_HK
dc.identifier.hkuros100309-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-22344451035&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume6en_HK
dc.identifier.isiWOS:000228346700001-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridCai, JJ=7403153560en_HK
dc.identifier.scopusauthoridSmith, DK=7410351143en_HK
dc.identifier.scopusauthoridXia, X=7402179513en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK
dc.identifier.citeulike2746746-

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