| Abstract |
Alignment of two-dimensional polyacrylamide electrophoresis (2D-PAGE) gels is of primary interest in the field of proteomics. In contrast with
previous approaches that considered only pair wise alignment, we consider algorithms for the alignment of a whole collection of gels. A synthetic
gel, containing some "ideal landmarks" is constructed together with a family of
transformations, so that for each gel from the collection there is a unique transformation that maps that gel into the synthetic gel in
such a way that the gel's landmarks are mapped into a very small neighborhoods of the
corresponding ideal landmarks. Both the ideal landmarks and the family of transformations are obtained as the solution
of a large-scale quadratic optimization problem, which can be efficiently solved by interior-point
methods. Alignment of families of 2D-gels is important for example in studies
assessing the effects of different treatments, when replicate gels from both
healthy and diseased subjects need to be collected and compared.
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