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

By T. Frickey, Andrei N. Lupas. 2004

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Citations in the corpus

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit (2020, methodology): “…Higgins, & Heringa, 2000)]; prediction of secondary structure and sequence features [Quick2D, PCOILS (Gruber, Sod-ing, & Lupas, 2006), TPRpred (Karpenahalli, Lupas, & Soding, 2007)]; and sequence classification [CLANS (Frickey & Lupas, 2004), MMseqs2 (Mirdita, Steinegger, & Sod-ing, 2019)].”
Cysteine‐rich domains related to Frizzled receptors and Hedgehog‐interacting proteins (2012, background): “The vertices (sequences) are then moved iteratively, based on the attractive forces designed to be proportional to the sequence similarities and a small repulsive force that serves to prevent collapse of sequences into one point.(35) Such a process can be run to equilibrium where movements of the ve”
Circoletto: visualizing sequence similarity with Circos (2010, background): “2008), and highly efficient graph layouts of large numbers of nodes representing sequences and edges representing similarity (Frickey and Lupas 2004).”
HHsenser: exhaustive transitive profile search using HMM–HMM comparison (2006, methodology): “Clustering of the sequences with CLANS resulted in eight major groups of bacterial transcription factors, six of which had been described before and two of which were groups of hypothetical proteins from cyanobacteria and proteobacteria.”
Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies (2009, background): “More recently, there have been efforts to use sequence similarity networks for more discrete sets of related proteins[8], and PFAM has released its classification of families into the more general clans , creating many three-level hierarchies bundling sequences into families, and families into…”
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis (2016, background): “Classification ANCESCON (12), BLASTClust (9), CLANS (56), ClubSub-P (57), daTAA (28), GCView (58), HHcluster (27), PHYLIP-NEIGHBOR (59)”
AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels. (2005, background): “Toxin-antitoxin operons appear to be involved in the maintenance of plasmids (“addiction modules”), as well as in the regulation of macromolecular synthesis during nutritional stress and in the programmed cell death of prokaryotes (Engelberg-Kulka and Glaser, 1999; Gerdes, 2000).”
The MPI Bioinformatics Toolkit for protein sequence analysis (2006, methodology): “CLANS clusters user-provided sequences based on BLAST pairwise similarities (29).”
A genomic and functional inventory of deubiquitinating enzymes. (2005, positive): “We used CLANS (Cluster analysis of sequences) software to visualize pairwise all-against-all sequence BLAST matches (Frickey and Lupas, 2004).”