:: DESCRIPTION
OSCAR (Open Source Cluster Application Resources) is a snapshot of the best known practices for building, programming and using a cluster. The toolkit is geared towards a modest sized cluster (50+ nodes) and features a wizard-based GUI for cluster installation.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif. It requires as input a multiple FASTA file. In the first step for each input sequence the base pair probability matrix of its secondary structure distribution is calculated (using RNAfold from the Vienna RNA package). Secondly, for each pair of base pair probability matrices a sequence-structure alignment is calculated using LocARNA. Lastly, a hierarchical cluster-tree (in NEWICK format) is derived by WPGMA clustering of the pairwise alignment distances and the optimal number of clusters is calculated from the tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Qgrid is a server provides cluster tree diagrams for proteins based on the charges on the atoms or hydrophobicity of a residue. Euclidean distances between charged atoms (or CA atoms of hydrophobic residues) are calculated and cluster tree diagrams are generated using hierarchical clustering method. These diagrams can be used to visually inspect hydrophobic and charged regions in proteins quickly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W104-7.
Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins.
Ahmad S, Sarai A.
:: DESCRIPTION
CCR XP tries to automate the detection and analysis of such clusters in protein structures.CCR XP is made of two input modules. CCR XP lite can be accessed directly (see query form on top), by uploading a PDB coordinate data or entering a PDB code and CCRs using default parameter settings for all protein chains in the coordinate file will be returned. The server will automatically (1) Extract fasta file from atom records (2) Find aligned sequences and calculate conservation scores (3) Cluster conserved residues and (4) Report several other structural properties of each residue as well as whole clusters, including their solvent accessibility that will allow to distinguish potential interface clusters from stabilizing core residues.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W398-401. doi: 10.1093/nar/gkq360. Epub 2010 May 10.
CCRXP: exploring clusters of conserved residues in protein structures.
Ahmad S, Keskin O, Mizuguchi K, Sarai A, Nussinov R.
:: DESCRIPTION
ClusterViz is a software to visualize the clustering process using the family of k-means algorithms. ClusterViz allows to cluster data while visualizing an up to three dimensional projection. The clustering process is visualized using OpenGL. As clustering algorithms the family of k-means algorithms is implemented, including mixture models.
::DEVELOPER
Alexander Schliep’s group for bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CTree has been designed for viewing, analyzing and editing phylogenetic trees. There is a particular emphasis on the analysis of clusters within such trees. Clusters are stored as individual data structures from which statistical data can be easily extracted.
::DEVELOPER
John Archer and David Robertson
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Archer J, Robertson DL.
CTree: comparison of clusters between phylogenetic trees made easy.
Bioinformatics (2007) 23 (21): 2952-2953.
:: DESCRIPTION
Modk-Prototypes is a software for clusters biological samples by simultaneously considering microarray gene expression data and classes of known phenotypic variables such as clinical chemistry evaluations and histopathologic observations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Syst Biol. 2007 Feb 23;1:15.
Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes.
Bushel PR, Wolfinger RD, Gibson G.
:: DESCRIPTION
GaneSh is a software to cluster expression data by Gibbs sampling procedure
::DEVELOPER
Bioinformatics & Systems Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Joshi, A., Van de Peer, Y., Michoel, T. (2008)
Analysis of a Gibbs sampler method for model based clustering of gene expression data.
Bioinformatics 24, 176-83.
:: DESCRIPTION
MotifOrganizer is designed to cluster large sets of DNA sequence motifs to identify common patterns. Different motif widths are allowed. It uses a two-stage divide-conquer-combine strategy to achieve scalability and efficiency.
::DEVELOPER
Steve Qin @ the Center for Statistical Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION