CLANS: a Java application for visualizing protein families based on pairwise similarity

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ID: 305996
2004
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Abstract
The main source of hypotheses on the structure and function of new proteins is their homology to proteins with known properties. Homologous relationships are typically established through sequence similarity searches, multiple alignments and phylogenetic reconstruction. In cases where the number of potential relationships is large, for example in P-loop NTPases with many thousands of members, alignments and phylogenies become computationally demanding, accumulate errors and lose resolution. In search of a better way to analyze relationships in large sequence datasets we have developed a Java application, CLANS (CLuster ANalysis of Sequences), which uses a version of the Fruchterman-Reingold graph layout algorithm to visualize pairwise sequence similarities in either two-dimensional or three-dimensional space.CLANS can be downloaded at http://protevo.eb.tuebingen.mpg.de/download.
Reference Key
openalex_W2138872556 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Tancred Frickey, Andrei N. Lupas
Journal BMC Bioinformatics
Year 2004
DOI
10.1093/bioinformatics/bth444
URL
https://academic.oup.com/bioinformatics/article-pdf/20/18/3702/48906481/bioinformatics_20_18_3702.pdf
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