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  PQP: Protein Quantification via shared peptides

  • Download the code. (C#, uses ILOG CPLEX 11.21 for solving linear programming).
    Please refer to the README file for the format of the input and the output files.

Download the input files and data for the simulations in Dost et. al., RECOMB 2009 . 

Supplemental Data: Inferred relative protein abundances in Arabidopsis root-knot nematode infection mass
spectrometry data obtained from Prof. Briggs lab, UCSD.     


 TCLUST: Tanimoto-coefficient based clustering

QNET: Querying protein interaction networks

You need Blast installed on the machine, the program calls Blast for sequence similarity. In the zipped folder , 3 PPI networks are included: fly (DIP, 2005), human Kegg and yeast (DIP, 2005).  You can also find some random trees extracted from yeast DIP network.


PAL: Sequence and Structural Alignment of Pseudoknotted RNA sequences.

Download sample RNA families. 

Detected novel members of families RF00165 and RF00507.

This site was last updated 11/07/09