Comparative Study on Global and Local Alignment methods

International Journal of Computer Trends and Technology (IJCTT)          
© - June Issue 2013 by IJCTT Journal
Volume-4 Issue-6                           
Year of Publication : 2013
Authors :Abhilash C B, Manjunath B Talawar


Abhilash C B, Manjunath B Talawar "Comparative Study on Global and Local Alignment methods"International Journal of Computer Trends and Technology (IJCTT),V4(6):1512-1520 June Issue 2013 .ISSN Published by Seventh Sense Research Group.

Abstract: - Pairwise sequence Alignment is one of the ways to arrange the two biological sequences to identify regions of similarity that may indicate functional, structural, and/or evolutionary relationship between the sequences (proteins or nucleic acids). In Pairwise sequence alignment we have two methods- Local Alignment (Smith-waterman algorithm) and Global Alignment (Needleman-Wunsch algorithm). In Local Alignment we treat two sequences may or may not be related and see whether a sub-string in one sequence align well with sub-string in the other, which can be applicable in searching for local similarities in large sequences. Whereas in Global Sequence Alignment we treat two Sequences as potentially equivalent, which identifies conserved regions and differences which can be applicable in comparing two genes with same functions. By using both alignment methods we are trying to find that on what conditions we can get the highest similarity between the pair of biological sequences. Smith-waterman and Needleman-Wunsch are the two algorithms used to check the percentage of similarity between the pair of biological Sequences.


[1]. Marc A. Schaib, Irene M.Kaplow, Marina Sirata and SerafimBatzaglau (2009). A Classifier Based approach to identify genetic similarity between diseases. International Journal of Computer Trends and Technology (IJCTT) – volume 4 Issue 6–June 2013
[2]. Needleman S.B. and Wunsch C.D. (1970) A general method application to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular BioLogy 48:443- 453.
[3]. KruskaJ J.B. (1983) An overview of sequence comparison, In Sankoff D. and Kruskal J.B., (ed.) Time warps, string edits and macromolecules: The theory and practice ofsequence comparison, ppl-44, Addison Wesley.
[4]. Gibbs AJ. and McIntyre G.A. (1970) The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. European Journal of Biochemistry 16:1-11.
[5]. McLachlan A.D. (1972) Repeating sequences and gene duplication in proteins. Journal Molecular Biology 64:417-437.
[6]. Smith T.F. and Waterman M.S. (19g I ) Comparison of bio-sequence. Advances in Applied Mathematics 2:482-489.
[7]. Boswell D.R. and Mclachlan A.D. (1984) Sequence comparison by exponentially damped alignment. Nucleic Acid Research 12:457-464.
[8]. Smith T.F. and Waterman M.S. (1981) Identification ofcommon molecular subsequences. Journal ofMolecular Biology 147: 195-197.
[9]. Sellers P.H. (1984) Pattern recognition in genetic sequences by mismatch density. Bulletin in Mathematical Biology 46:705-708
[10].Waterman M.S. and Jones R. (1990) Consensus methods for DNA and protein sequences alignment, in Molecular Evolution: Computer Analysis ofProtein and Nucleic Acid Sequences, (eds. Doolittle R.E) 183:221-237, Academic Press, Inc., San Diego.

Keywords — Local Alignment, Global Alignment, Needleman-wunsch, Smiths-waterman .