BiblioSpec 2.0 – Creat and Search MS/MS Peptide Spectrum Libraries

BiblioSpec 2.0

:: DESCRIPTION

BiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra.

::DEVELOPER

MacCoss Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 BiblioSpec

:: MORE INFORMATION

Citation

Using BiblioSpec for creating and searching tandem MS peptide libraries.
Frewen B, MacCoss MJ.
Curr Protoc Bioinformatics. 2007 Dec;Chapter 13:Unit 13.7.

clusterMaker2 1.3.1 – Creat and Visualize Cytoscape Clusters

clusterMaker2 1.3.1

:: DESCRIPTION

UCSF clusterMaker is a Cytoscape plugin that unifies different clustering techniques and displays into a single interface. Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and k-means for clustering expression or genetic data; and MCL, transitivity clustering, affinity propagation, MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity or distance values. Hierarchical, k-medoid, AutoSOME, and k-means clusters may be displayed as hierarchical groups of nodes or as heat maps. All of the network partitioning cluster algorithms create collapsible “meta nodes” to allow interactive exploration of the putative family associations within the Cytoscape network, and results may also be shown as a separate network containing only the intra-cluster edges, or with inter-cluster edges added back

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

clusterMaker

:: REQUIREMENTS

:: DOWNLOAD

 clusterMaker

:: MORE INFORMATION

Citation:

clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE.
BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.