Informatics Publishing Limited

Archana Verma ¹, Rajendra Kumar Bharti ¹, R. K. Singh ²

Affiliations
1 Uttarakhand Technical University, Dehradun, IN
2 ECE Department, B.C.T. Kumaon Engineering College, Dwarahat, Almora, Uttarakhand, IN

Abstract

Sequence assembly is a difficult problem whose importance is continuously growing even recently the cost of sequencing has dramatically decreased. The computer simulation for the evolution of sequence assembly of linear sequences have demonstrated the importance of recombination of blocks of sequences. Repeated cycles of point mutagenesis, recombination and selection should allow in "in vitro" molecular evolution of complex sequences, such as proteins. A method for the reassembly of genes from their random DNA fragments, resulting in "in vitro" recombination is reported by Stemmer and there are some laboratory techniques also available that results in reliable sequencing of approximately 500 nucleotides (500-mers). If we have lots and lots of 500-mers than the original genome (from which these 500-mers may be obtained) sequence will be assembled. All such methods are based on image fragmentation reassembly. In this paper we are proposing a technique that is based on tabular form. In the proposed technique we develop a table, which has four rows and two columns and contained information about the base character and position of the base character in the DNA sequence.

Keywords

Fragment, Genomes, In Vitro, Mutagenesis, Nucleotide, Reassembly, Sequence.

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Rajendra Kumar Bharti ¹, Archana Verma ¹, R. K. Singh ²

Affiliations
1 Department of Computer Science & Engineering, B.C.T. Kumaon Engineering College, Dwarahat, Almora, Uttarakhand, IN
2 ECE Department, B.C.T. Kumaon Engineering College, Dwarahat, Almora, Uttarakhand, IN

Abstract

Genome may contain several copies of the same gene. Although human genome contains about 3 billion base pairs, only 3% of it encodes protein. There are only about 25000 genes in human genome which encode about 100000 proteins by alternative splicing. Biological sequences are commonly of two types - unique and repeated. We are utilizing these properties of the sequences. The earlier algorithms either work on unique repeat or repeated repeat sequence. We are merging both methodologies to develop a new algorithm which collectively compress both type of sequences, i.e. we can apply the same compression algorithm on all types of sequences. This will definitely reduce our effort for developing different algorithm and it will be easier to apply one single algorithm rather using different algorithm. In this paper, a Biological sequence compression is proposed to compress both unique sequences, which are repeated in one area, and repeated sequences that are interspersed throughout the genome. The algorithm is also compared with existing ones and it is found to achieve better compression ratio than other.

Keywords

Genome, Sequence, Uniqueness, Compression Ratio, DNA Compress, Gen Compress, LUT, Base Pair.

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