The coming of the most recent generations of sequencing technologies  has opened a lot of new research chances in the fields of science (biology) and medication, including cell Deoxyribonucleic Acid (DNA) sequencing, gene disclosure and evolutionary connections. These sophisticated technologies have helped the exponential development of biological information that is accessible for specialists. For example, the Genbank  has multiplied its information measure at regular intervals (approximately 18 months) and in its latest release of February 2014 it included over 158 × 109 base pairs (bps) from a few distinctive species.
To aid the researcher in the extraction of handy data and in the understanding of the immense estimated sequence databases, a set of alignment algorithms (e.g. the generally utilized Smith–Waterman (S–W)  and Steven-Song optimized [ ] algorithms) have been produced to take care of numerous open issues in the field of bioinformatics, for example, (1) DNA re-sequencing, where genome gathering is carried out against a reference genome; (2) Multiple Sequence Alignment (MSA), where various genomes are adjusted to perform genome annotation; and (3) Gene discovering, where Ribonucleic Acid (RNA) sequences are adjusted against the living being genome to recognize new genes.
At present, a basic sequencing methodology is dependent upon the provision of High Throughput Short Read (HTSR) technologies , to decrease the expense of the sequencing procedure. This methodology comprises of cutting the DNA pieces under analysis into shorter sections called short reads, which are exclusively sequenced and aligned against a reference sequence.
Currently, the three most essential HTSR sequencing platforms are: the Solexa 1g Sequencer (lllumina), the GS FLX Genome Analyzer (454), and the Solid Sequencer (Applied Biosystems). The biochemistry engineering underlying each of these platforms prompts altogether different attributes, in terms of throughput, short reads length, and raw errors. In any case, freely of the embraced platform, the length of the short reads processed by these platforms is small when contrasted with past generation sequencing technologies and much smaller than the original completed DNA sequence. Though, the big volume of information that is created and the requirement to align these short reads to huge reference genomes constrains an immediate and credulous provision of standard Dynamic Programming (DP) methods. One straightforward example of a common challenge comes from the necessity to align up to 100 million short reads against a reference genome that could be as substantial as 3 Gbp. For the SOLiD sequencer, with reads as short as 30 bps, this relates to the processing of 100 million grids of size 3 × 109 × 30, which brings about a computational...