Abstract: With the rapid development in the field of life
sciences and the flooding of genomic information, the need for faster
and scalable searching methods has become urgent. One of the
approaches that were investigated is indexing. The indexing methods
have been categorized into three categories which are the lengthbased
index algorithms, transformation-based algorithms and mixed
techniques-based algorithms. In this research, we focused on the
transformation based methods. We embedded the N-gram method
into the transformation-based method to build an inverted index
table. We then applied the parallel methods to speed up the index
building time and to reduce the overall retrieval time when querying
the genomic database. Our experiments show that the use of N-Gram
transformation algorithm is an economical solution; it saves time and
space too. The result shows that the size of the index is smaller than
the size of the dataset when the size of N-Gram is 5 and 6. The
parallel N-Gram transformation algorithm-s results indicate that the
uses of parallel programming with large dataset are promising which
can be improved further.