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In transport control protocol (TCP) over optical burst switching (OBS) networks, TCP window size and OBS parameters, including assembly period and burst dropping probability, will impact the network performance. In this paper, a parameter window data dropping probability(WDDP), is defined to analyze the impact of the assembly and the burst loss on the network performance in terms of the round trip time and the throughput. To reduce the WDDP without introducing the extra assembly delay penalty, we propose a novel TCP window based flow-oriented assembly algorithm dynamic assembly period (DAP). In the traditional OBS assembly algorithms, the packets with the same destination and class of service (CoS) are assembled into the same burst, i.e., the packets from different sources will be assembled into one burst. In that case, one burst loss will influence multiple TCP sources. In DAP, the packets from one TCP connection are assembled into bursts, which can avoid the above situation. Through comparing the two consecutive burst lengths, DAP can track the variation of TCP window dynamically and update the assembly period for the next assembly. In addition, the ingress node architecture for the flow-oriented assembly is designed. The performance of DAP is evaluated and compared with that of fixed assembly period (FAP) over a single TCP connection and multiple TCP connections. The results show that DAP performs better than FAP at almost the whole range of burst dropping probability.