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Analyses, interpretation and integration of the information are the high level cognition skills, and mastering these knowledge integration skills is the main goal of science education. We've employed a project-based assessment to facilitate such learning in a bioinformatics course. This assessment is presented as a set of designed assignments, which is based on a protein sequence with unidentified function. A series of criteria have been formulated to serve as the learning scaffold for students. The criteria are intended to foster the students' ability in tool selection, data analyses and output interpretation. In the second stage, the students in group of three are asked to integrate and explore their results to construct a research-oriented project. The project is displayed in a poster format and reviewed by experts and peers. Through this process, students successfully demonstrate their achievement in choosing tools, interpreting data, integrating results, building new models, and formulating testable hypothesis.