Abstract:
BACKGROUND: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. RESULTS:We present Sili2DGel 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. In the algorithm, 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.). We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects. CONCLUSION:Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies) of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Pérès S,Molina L,Salvetat N,Granier C,Molina Fdoi
10.1186/1471-2105-9-460subject
Has Abstractpub_date
2008-10-28 00:00:00pages
460issn
1471-2105pii
1471-2105-9-460journal_volume
9pub_type
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