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This paper presents a new algorithm for generation of attack signatures based on sequence alignment. The algorithm is composed of two parts: a local alignment algorithm-GASBSLA (Generation of Attack Signatures Based on Sequence Local Alignment) and a multi-sequence alignment algorithm-TGMSA (Tri-stage Gradual Multi-Sequence Alignment). With the inspiration of sequence alignment used in Bioinformatics, GASBSLA replaces global alignment and constant weight penalty model by local alignment and affine penalty model to improve the generality of attack signatures. TGMSA presents a new pruning policy to make the algorithm more insensitive to noises in the generation of attack signatures. In this paper, GASBSLA and TGMSA are described in detail and validated by experiments.