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 1.1 (10/30/2009) . Download: software
  • New features include: 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

.