Algorithms for String Comparison in DNA Sequences.

String comparison algorithms are the pathway to determine various characteristics of genomes, DNA or protein sequences. In this article, three different existing algorithms are described with some additional features, which provide better performance in terms of different performance measures. At first, a dynamic programming algorithm for small k-mer is described which is based on the existing hash table SSAHA method to search large DNA database that gives better run time for small k-mer. Then a genome alignment algorithm is described that will find out MUMs (Maximal Unique Match) where Burrows Wheeler Transform matrix and an additional data structure FM (Ferragina and Manzini) index are used instead of suffix tree. Finally, an improved version of existing Sibelia tool’s algorithm is proposed to find out synteny blocks from microbial genome, where existing algorithm determines only the loops greater than the size of bulges whereas the proposed algorithm determines loops of all sizes.