A Study on Suffix Trees and Their Applications in Genome Sequences Using MUMmer

A suffix tree is a data structure that stores a string of text. In bioinformatics, the suffix trees can be used as a tool to align the entire genomes of closely related organisms, to compare sequence assemblies at different phases and to compare and analyze the results. This paper focuses on the aligning of various whole genome sequences, using suffix trees. In the present investigation, the implementations of the suffix trees are discussed, focusing on two models for comparison and alignment. The first model is multiple sequence alignment based on a suffix tree and center-star strategy (MASC), which is a leading method to find solutions for the alignment of evolutionarily related sentences, considering evolutionary events like mutations, insertions, deletions and rearrangement. MASC applies to deoxyribonucleic acid (DNA), ribonucleic acid (RNA) and protein sequences. The second model maximal unique match (MUMmer) is discussed. Multiple genome alignment tools (Clustal Omega, Clustal W, MUSCLE, MAFFT and Mauve) are compared with MUMmer and are proving the efficiency of MUMmer, because of the use of the suffix trees.