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MSuPDA: A Memory Efficient Algorithm for Sequence Alignment

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Abstract

Space complexity is a million dollar question in DNA sequence alignments. In this regard, memory saving under pushdown automata can help to reduce the occupied spaces in computer memory. Our proposed process is that anchor seed (AS) will be selected from given data set of nucleotide base pairs for local sequence alignment. Quick splitting techniques will separate the AS from all the DNA genome segments. Selected AS will be placed to pushdown automata’s (PDA) input unit. Whole DNA genome segments will be placed into PDA’s stack. AS from input unit will be matched with the DNA genome segments from stack of PDA. Match, mismatch and indel of nucleotides will be popped from the stack under the control unit of pushdown automata. During the POP operation on stack, it will free the memory cell occupied by the nucleotide base pair.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Chittagong University of Engineering and Technology, Cuet Road, Chittagong, 4349, Bangladesh

    Mohammad Ibrahim Khan, Md. Sarwar Kamal & Linkon Chowdhury

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  1. Mohammad Ibrahim Khan
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  2. Md. Sarwar Kamal
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  3. Linkon Chowdhury
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Correspondence to Linkon Chowdhury.

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Khan, M.I., Kamal, M.S. & Chowdhury, L. MSuPDA: A Memory Efficient Algorithm for Sequence Alignment. Interdiscip Sci Comput Life Sci 8, 84–94 (2016). https://doi.org/10.1007/s12539-015-0275-8

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  • DOI: https://doi.org/10.1007/s12539-015-0275-8

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