In this paper, we have presented a method for identifying missing items known as gaps in the student answers by comparing them against the corresponding model answer/reference answers, automatically. The gaps can be identified at word, phrase or sentence level. The identified gaps are useful in providing feedback to the students for formative assessment. The problem of gap identification has been modelled as an alignment of a pair of directed graphs representing a student answer and the corresponding model answer for a given question. To validate the proposed approach, the gap annotated student answers considering answers from three widely known datasets in the short answer grading domain, namely, University of North Texas (UNT), SciEntsBank, and Beetle have been developed and this gap annotated student answers' dataset is available at: https://github.com/sahuarchana7/gaps-answers-dataset. Evaluation metrics used in the traditional machine learning tasks have been adopted to evaluate the task of gap identification. Though performance of the proposed approach varies across the datasets and the types of the answers, overall the performance is observed to be promising.