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Species Counting Software

By Erez Persi.


The downloadable files in this page are Matlab source files for performing the species counting algorithm on Proteromic data as described in Persi et al. 2010 (see reference below).

Source Files Download

The Species Counting source code, written in Matlab, is freely available for academic use under the following registration and license agreement. It is also available for non-academic use under appropriate licensing. Please contact David Horn

download all files in zip format or the separate files here: - contains all the files below
Main.m - main function that accepts Protein sequences, a deterministic peptide pattern (SP) that is common to all the Proteins,
and the number of iterations that should be sufficient for convergence. Output: a reduced set of fused proteins that are all inconsistent.
sp_pp_aline.m - SP-alignment function. Alignes a cell array of Proteins by the SP that is common to all of them, and produces a consistent Matrix relationship among them.
species_counting_byId_merge.m - Preforms one step of Proteins fusion according to their consistency Matrix.
merge.m - merge any two proteins that have a consistency relationship.
count_mutation.m - counts the number of different Amino-acids for any pair of proteins (upper-triangle matrix).
get_count_by_mutation_dis.m - counts the number of inconsistencies for minimal number of differences that is larger than some #.
Algo.doc - step by step example of how the algorithm work for the simple example that is given in the paper.