BLASTAssemb: An approach to construct genetic elements using BLAST

Abstract

With the availability of recent next generation sequencing technologies and cheap price, genome of different organisms is now being sequenced frequently. Therefore, quick assembling of a genetic element from the raw genome generated through the sequencing technologies has become necessary for better understanding of different biological systems. This paper proposes an algorithm for constructing genetic elements from raw genome using reference sequences. For this, we considered a weighted frequency based consensus making mechanism. Furthermore, we have used BLAST (Basic local alignment search tool), a well known tool to the community of bioinformaticians, in this regard. The proposed method, thus applies the capability of BLAST, which enables the construction of genetic elements from raw sequences. For evaluating our algorithm, we have chosen Pokkali (a verity of rice) raw genome and few promoters of Japonica (another verity of rice) as our reference data. Experimental results demonstrated that our proposed algorithm could accurately construct the promoter sequences of Pokkali from its raw genome sequences.