MSuPDA: A Memory Efficient Algorithm for Sequence Alignment.

Khan, MI; Kamal, MS; Chowdhury, L

MSuPDA: A Memory Efficient Algorithm for Sequence Alignment.

Khan, MI Kamal, MS Chowdhury, L

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Publisher:: Springer Nature
Publication Type:: Journal Article
Citation:: Interdiscip Sci, 2016, 8, (1), pp. 84-94
Issue Date:: 2016-03

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Field	Value	Language
dc.contributor.author	Khan, MI
dc.contributor.author	Kamal, MS
dc.contributor.author	Chowdhury, L
dc.date.accessioned	2023-03-07T02:52:04Z
dc.date.available	2014-11-03
dc.date.available	2023-03-07T02:52:04Z
dc.date.issued	2016-03
dc.identifier.citation	Interdiscip Sci, 2016, 8, (1), pp. 84-94
dc.identifier.issn	1913-2751
dc.identifier.issn	1867-1462
dc.identifier.uri	http://hdl.handle.net/10453/166690
dc.description.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.
dc.format	Print-Electronic
dc.language	eng
dc.publisher	Springer Nature
dc.relation.ispartof	Interdiscip Sci
dc.relation.isbasedon	10.1007/s12539-015-0275-8
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject.mesh	Algorithms
dc.subject.mesh	Base Sequence
dc.subject.mesh	Molecular Sequence Data
dc.subject.mesh	Sequence Alignment
dc.subject.mesh	Sequence Alignment
dc.subject.mesh	Base Sequence
dc.subject.mesh	Algorithms
dc.subject.mesh	Molecular Sequence Data
dc.subject.mesh	Algorithms
dc.subject.mesh	Base Sequence
dc.subject.mesh	Molecular Sequence Data
dc.subject.mesh	Sequence Alignment
dc.title	MSuPDA: A Memory Efficient Algorithm for Sequence Alignment.
dc.type	Journal Article
utslib.citation.volume	8
utslib.location.activity	Germany
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology/School of Computer Science
utslib.copyright.status	closed_access	*
dc.date.updated	2023-03-07T02:52:03Z
pubs.issue	1
pubs.publication-status	Published
pubs.volume	8
utslib.citation.issue	1

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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http://hdl.handle.net/10453/166690