Comparison of cancer treatment protocols against patient history is important to assess the efficiency of chemotherapy protocols. However, manual identification of protocols is not possible when considering a large population of patients. This paper proposes a new method called ATLAS (Analysis of Treatment Lines using Alignment of Sequences) to tackle the problem related to protocol identification using claim databases as data input. The proposed algorithm is an extension of the Smith-Waterman algorithm and allows to compare any patient's medical history against a list of theoretical protocols taking into account temporal information in sequences as well as missing data. Numerical experiments show that the proposed method could identify the right protocol in over 95% of the cases for realistically noised sequences (15,000 generated patients aligned with 15 protocols). The method is meant to be used as a decision aid tool for practitioners.