software

Geometric Analysis of Structural Variants (GASV)

Software for classification and comparison of strutural variants measured via paired-end sequencing and/or array-CGH. The method is described in the following paper:

S. Sindi, E. Helman, A. Bashir, B.J. Raphael. (2009)A Geometric Approach for
Classification and Comparison of Structural Variants.Bioinformatics. 25: i222-i230. (Special issue for the Joint 17th Annual International Conference on Intelligent Systems in Molecular Biology and 8th Annual International European Conference on Computational Biology (ISMB/ECCB 09)). Publisher Link

  • Description of the software: README.
  • Version 1.3 (1/19/2010) . Download: software
  • Example BAM file
  • New in Version 1.3: New output formats, streamlining of BAM file handling, bug fixes.
  • New in Version 1.2 (11/30/2009): Improved handling of SAM/BAM alignment files, speed improvements, maxCliqueSize option.
  • New in Version 1.1: a preprocessor for SAM/BAM files, aCGH comparison, fusion gene detection, and more.
Motif Description Length (MoDL):

MoDL finds mutliple motifs in a set of phosphorylated peptides, and is described in the following paper:

A. Ritz, G. Shakhnarovich, A.R. Salomon, and B. Raphael. Discovery of Phosphorylation Motif Mixtures in Phosphoproteomics Data. (2009) Bioinformatics. 25(1):14-21. Publisher Link

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