Indexing Genome with the External Construction of Compressed Suffix Tree Using LCP Array

Abstract

We are proposing the genome indexing algorithm, which depends upon compressed form of suffix trees, in which every node has four parts; suffix array number, suffix start number, LCP count, and a pointer to another node. The proposed algorithm does not use the whole suffix array, it just takes some necessary information like LCP of two suffix array, compare them and suffix start number, to align the suffix to proper position and suffix array number to distinguish among all the partitions. The use of compressed suffix array minimizes the number of trees, eventually; it also minimizes the random access to input data, as it creates the compressed suffix tree for two suffix arrays using pairwise sorting, sequentially.