Sequence alignment of extra chromosomal deoxyribosenucleic acid base pairs of bacteria and plant: possible mechanism of genome rearrangements

Computer generated sequence alignment became a conventional tool in bioinformatics. SIMis one of the methods for determining similarity between two sequences through a pair-wise sequencealignment. However, most of the conventional tools lack the ability of incorporating biological propertiesinto the alignment result which often leads to incorrect alignment. In this paper, we used a pair-wisealignment system called SIM that incorporates biological properties into the algorithm so that it cansuggest an appropriate sequence alignment based on the given nucleotide base pairs. SIM indicatednucleotide sequences alignments and suggested massive rearrangements of extra chromosomal, whichcan be extrapolated to total genome rearrangements.