title: SeqCompress: an algorithm for biological sequence compression.
abstract: The growth of Next Generation Sequencing technologies presents significant research challenges, specifically to design bioinformatics tools that handle massive amount of data efficiently. Biological sequence data storage cost has become a noticeable proportion of total cost in the generation and analysis. Particularly increase in DNA sequencing rate is significantly outstripping the rate of increase in disk storage capacity, which may go beyond the limit of storage capacity. It is essential to develop algorithms that handle large data sets via better memory management. This article presents a DNA sequence compression algorithm SeqCompress that copes with the space complexity of biological sequences. The algorithm is based on lossless data compression and uses statistical model as well as arithmetic coding to compress DNA sequences. The proposed algorithm is compared with recent specialized compression tools for biological sequences. Experimental results show that proposed algorithm has better compression gain as compared to other existing algorithms.
authors.affiliation: Department of Computing and Technology, Iqra University, Islamabad, Pakistan. Electronic address: sardaraz@hotmail.com.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Sardaraz
authors.affiliation: Department of Computer Science, University of Wah, Wah Cantt, Pakistan. Electronic address: muhammad.tahir@uow.edu.pk.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Tahir
authors.affiliation: Department of Electrical Engineering, National University, Islamabad, Pakistan. Electronic address: ata.ikram@nu.edu.pk.
authors.forename: Ataul Aziz
authors.initials: AA
authors.lastname: Ikram
authors.affiliation: Department of Electrical Engineering, University of Bridgeport, Bridgeport, USA. Electronic address: h.bajwa@bridgeport.edu.
authors.forename: Hassan
authors.initials: H
authors.lastname: Bajwa
mesh_terms: D000465:Algorithms; D044962:Data Compression / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods
keywords: Compression; DNA; Genome sequences; NGS technologies