Fully Automated Detection of Landmark Spot Pairs using the Topology of Both the First and the Second Neighbor Spots in Two-Dimensional Electrophoresis

摘要

Some spot matching algorithms in two-dimensional electrophoresis (2-DE) require landmark spot pairs from the beginning and they are supposed to be selected manually only by researchers. The 2-dimensional gel images are stretched or shrunk before comparing two images - reference and target gel. Some algorithms use only a single landmark spot pair at the starting point of matching. It is used as the starting point for spot matching. In this paper, a fully automated method of detecting landmark spot pairs is proposed. It takes advantage of the first and the second neighbor spots for every spot pair to determine the best landmark spot pairs. In our previous research, it only depends on the topology of the first neighbor spots to find matched spot pairs but it has outcome more false positive results when the number of spots increases. Even though the proposed method can produce more complex topologies due to two kinds of neighbor spots, whereas the possibility of appearing similar topologies for unmatched spots can be reduced. This means that the highly reliable matched spot pairs can be detected automatically. Therefore, the best landmark spot pairs by a fully automated manner can be obtained using the proposed algorithm.