Comparison of nucleotide DNA alignment search programmes

This paper evaluates the performance of search alignment tools using Blast and MegaBlast obtained from the National Center for Biotechnology Information (NCBI) website. The main objective is to articulate clearly the dependencies of the different parameters on the performance of the search alignment tool. The parameters that are of interest will be the seed size used as well as the size of the nucleotide input sequence. Four experiments were conducted using programmes available on NCBI website. The first two experiments preselect two input nucleotide query sequences of various lengths belonging to the rat's organism and searched the source databases for matches. The source databases selected were the RAT EST and the MOUSE EST. The third experiment used an input query sequence string of a large nucleotide belonging to the rat's organism and searched against the Mouse genome. The fourth experiment used an input query sequence string belonging to another Hessian fly species and it was searched against the MOUSE EST. Experimental results using Gapped Blast version 2.2.6 and MegaBlast showed that the performance timing of both search engines was comparable. Also, the number of sequences found for a single seed size was much higher in MegaBlast compared to Blast.