#
Species Counting Software

By
Erez Persi.
## Overview

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:

SC.zip - 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.

## References