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With the growing demand for visual information of rich content, effective and efficient manipulations of large video databases are increasingly desired. Many investigations have been made on content-based video retrieval. However, despite the importance, video subsequence identification, which is to find the similar content to a short query clip from a long video sequence, has not been well addressed. This paper presents a graph transformation and matching approach to this problem, with extension to identify the occurrence of potentially different ordering or length due to content editing. With a novel batch query algorithm to retrieve similar frames, the mapping relationship between the query and database video is first represented by a bipartite graph. The densely matched parts along the long sequence are then extracted, followed by a filter-and-refine search strategy to prune some irrelevant subsequences. During the filtering stage, maximum size matching is deployed for each subgraph constructed by the query and candidate subsequence to obtain a smaller set of candidates. During the refinement stage, sub-maximum similarity matching is devised to identify the subsequence with the highest aggregate score from all candidates, according to a robust video similarity model that incorporates visual content, temporal order, and frame alignment information. The performance studies conducted on a long video recording of 50 hours validate that our approach is promising in terms of both search accuracy and speed.