{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T07:54:23Z","timestamp":1772092463430,"version":"3.50.1"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The R package <jats:italic>bios2mds<\/jats:italic> (from BIOlogical Sequences to MultiDimensional Scaling) has been designed to analyze multiple sequence alignments by MDS. <jats:italic>Bios2mds<\/jats:italic> 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 <jats:italic>K<\/jats:italic>-means clustering in the MDS derived sequence space. Most importantly, <jats:italic>bios2mds<\/jats:italic> includes a function that projects supplementary elements (a.k.a. \u201cout of sample\u201d elements) onto the space defined by reference or \u201cactive\u201d 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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The <jats:italic>bios2mds<\/jats:italic> 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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-133","type":"journal-article","created":{"date-parts":[[2012,6,27]],"date-time":"2012-06-27T13:14:32Z","timestamp":1340802872000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling"],"prefix":"10.1186","volume":"13","author":[{"given":"Julien","family":"Pel\u00e9","sequence":"first","affiliation":[]},{"given":"Jean-Michel","family":"B\u00e9cu","sequence":"additional","affiliation":[]},{"given":"Herv\u00e9","family":"Abdi","sequence":"additional","affiliation":[]},{"given":"Marie","family":"Chabbert","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,6,15]]},"reference":[{"key":"5243_CR1","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1007\/BF02941116","volume":"24","author":"C B-Rao","year":"1999","unstructured":"B-Rao C, Majumdar KC: Reconstruction of phylogenetic relationships. 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