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Title

 

 

 

 

A comparison of four pair-wise sequence alignment methods

 

Authors

Nadia Essoussi1 and Sondes Fayech1, *

 

Affiliation

1Department of Computer Science, Higher Institute of Management, Tunis, Tunisia

 

Phone

216 71 58 85 14

 

Fax

216 71 58 84 87

 

Email

sondes.fayech@ isg.rnu.tn; * Corresponding author

 

Article Type

Hypothesis

 

Date

received August 24, 2007; revised Novemeber 23, 2007; accepted December 09, 2007; published online December 28, 2007

 

Abstract

Protein sequence alignment has become an essential task in modern molecular biology research. A number of alignment techniques have been documented in literature and their corresponding tools are made available as freeware and commercial software. The choice and use of these tools for sequence alignment through the complete interpretation of alignment results is often considered non-trivial by end-users with limited skill in Bioinformatics algorithm development. Here, we discuss the comparison of sequence alignment techniques based on dynamic programming (N-W, S-W) and heuristics (LFASTA, BL2SEQ) for four sets of sequence data towards an educational purpose. The analysis suggests that heuristics based methods are faster than dynamic programming methods in alignment speed.

 

Keywords

sequence alignment techniques; Needleman & Wunsch; Smith & Waterman; LFASTA; BL2SEQ

 

Citation

Essoussi & Fayech, Bioinformation 2(4): 166-168 (2007)

 

Edited by

P. Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.