Bios2mds: An R Package for Comparing Orthologous Protein Families by Metric Multidimensional Scaling

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dc.contributor.ISNI0000 0001 1648 3631 (Abdi, H.)
dc.contributor.LCNA94060324‏ (Abdi)
dc.contributor.authorPele, Julienen_US
dc.contributor.authorBecu, Jean-Michelen_US
dc.contributor.authorAbdi, Hervéen_US
dc.contributor.authorChabbert, Marieen_US
dc.date.accessioned2013-10-04T19:40:43Z
dc.date.available2013-10-04T19:40:43Z
dc.date.created2012-06-15
dc.description.abstractBackground: The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS). Applied to protein families, MDS provides information complementary to the information derived from tree-based methods. Moreover, MDS gives a unique opportunity to compare orthologous sequence sets because it can add supplementary elements to a reference space.Results: The R package bios2mds (from BIOlogical Sequences to MultiDimensional Scaling) has been designed to analyze multiple sequence alignments by MDS. Bios2mds starts with a sequence alignment, builds a matrix of distances between the aligned sequences, and represents this matrix by MDS to visualize a sequence space. This package also offers the possibility of performing K-means clustering in the MDS derived sequence space. Most importantly, bios2mds includes a function that projects supplementary elements (a.k.a. " out of sample" elements) onto the space defined by reference or " active" elements. Orthologous sequence sets can thus be compared in a straightforward way. The data analysis and visualization tools have been specifically designed for an easy monitoring of the evolutionary drift of protein sub-families.Conclusions: The bios2mds package provides the tools for a complete integrated pipeline aimed at the MDS analysis of multiple sets of orthologous sequences in the R statistical environment. In addition, as the analysis can be carried out from user provided matrices, the projection function can be widely used on any kind of data.en_US
dc.identifier.bibliographicCitationPele, Julien, Jean-Michel Becu, Hervé Abdi, and Marie Chabbert. 2012. "Bios2mds: An R package for comparing orthologous protein families by metric multidimensional scaling." BMC Bioinformatics 13(133).en_US
dc.identifier.issn1471-2105en_US
dc.identifier.issue1en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/2864
dc.identifier.volume13en_US
dc.relation.urihttp://dx.doi.org/10.1186/1471-2105-13-133en_US
dc.rightsCC BY 2.0 (Attribution) © 2012 Pelé et al.; e BioMed Central Ltd.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/2.0/en_US
dc.source.journalBMC Bioinformaticsen_US
dc.subjectEvolutionen_US
dc.subjectPhylogenyen_US
dc.subjectProteinsen_US
dc.subjectR (Computer program language)en_US
dc.titleBios2mds: An R Package for Comparing Orthologous Protein Families by Metric Multidimensional Scalingen_US
dc.typeTexten_US
dc.type.genrearticleen_US

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