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

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.