In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user.

Sili2DGel (download) an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. It is based on graph theory in which the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). To run Sili2DGel, you have to install JRE. Sili2DGel needs a recursive alignment result file (tabular file of this form) and spot coordinate file (tabular file of this form). Gamma is comprised between 0 and 1; strengh is comprised between 0 and 2.

Sili2DGel returns 5 files:

Graph data and graph result files (save as .tlp) which can be viewed with Tulip software.
Synthetic gel (save as .svg) which can be viewed with an explorer.
Alignment result and rejected spot files (save as .xls).