ArticleBMC bioinformatics2012
Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- In-Host HEV Quasispecies Evolution Shows the Limits of Mutagenic Antiviral Treatments.International journal of molecular sciences · 2023Article
- Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae).Scientific reports · 2023Article
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- Bacteriocin Production Correlates with Epidemiological Prevalence of Phylotype I Sequevar 18 Ralstonia pseudosolanacearum in Madagascar.Applied and environmental microbiology · 2023Article
- Homology Modeling in the Twilight Zone: Improved Accuracy by Sequence Space Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Plasma virome dynamics in chronic hepatitis B virus infected patients.Frontiers in microbiology · 2023Article
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- Genomic Determinants Potentially Associated with Clinical Manifestations of Human-Pathogenic Tick-Borne Flaviviruses.International journal of molecular sciences · 2022Article
- Generalizable strategy to analyze domains in the context of parent protein architecture: A CheW case study.Proteins · 2022Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsThe 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.
conclusionsThe 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.
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