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A Noble Approach on Bioinformatics: Smart Sequence Alignment Algorithm applying DNA Replication (SSAADR)

Paramita Basak Upama, Jarin Tasnim Khan, Zeba Yasmin, Farah Zemim, Nazmus Sakib Published in Algorithms

International Journal of Applied Information Systems
Year of Publication: 2014
© 2013 by IJAIS Journal
10.5120/ijais14-451279
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  1. Paramita Basak Upama, Jarin Tasnim Khan, Zeba Yasmin, Farah Zemim and Nazmus Sakib. Article: A Noble Approach on Bioinformatics: Smart Sequence Alignment Algorithm applying DNA Replication (SSAADR). International Journal of Applied Information Systems 8(1):23-28, December 2014. BibTeX

    @article{key:article,
    	author = "Paramita Basak Upama and Jarin Tasnim Khan and Zeba Yasmin and Farah Zemim and Nazmus Sakib",
    	title = "Article: A Noble Approach on Bioinformatics: Smart Sequence Alignment Algorithm applying DNA Replication (SSAADR)",
    	journal = "International Journal of Applied Information Systems",
    	year = 2014,
    	volume = 8,
    	number = 1,
    	pages = "23-28",
    	month = "December",
    	note = "Published by Foundation of Computer Science, New York, USA"
    }
    

Abstract

Alignment generally means lining up characters of strings, allowing matches and mismatches and also the characters of one string to be placed opposite spaces made in opposing strings. Sequence alignment arises in many fields, such as: molecular biology, inexact text matching (e. g. spell checkers; web page search), speech recognition and many more. This Paper presents a new implemented algorithm for sequence alignment based on the concepts of some already established algorithms of Bioinformatics which is named as "Smart Sequence Alignment Algorithm applying DNA Replication", in short "SSAADR". It aligns two sequences of any length, based on filling up a matrix of size m X n where m is the length of the first sequence and n is the length of the second sequence, and using the techniques of both global and local alignment. To make the proposed algorithm faster, the theory of DNA replication has also been introduced here, according to which, while using the alternative sequences of both DNA sequences instead of the original ones, the execution time of the proposed algorithm SSAADR decreases immensely.

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Keywords

Sequence alignment, DNA, RNA, Dynamic Algorithms, Z Algorithm, Boyer-Moore Algorithm, Needleman-Wunsch (NW) Algorithm and Smith-Waterman (SW) Algorithm.