Beyond Bioinformatics

Title

A comparison of four pair-wise sequence alignment methods

Authors

Nadia Essoussi¹ and Sondes Fayech^{1, *}

Affiliation

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

216 71 58 85 14

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

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.

Citation

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

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.