NDLI: Improved algorithms for DNA sequence alignment and revision of scoring matrix

Content Provider	IEEE Xplore Digital Library
Author	Bandyopadhyay, S.S. Paul, S. Konar, A.
Copyright Year	2005
Description	Author affiliation: Dept. of Electron. & Telecommun. Dept., Jadavpur Univ., Kolkata, India (Bandyopadhyay, S.S.; Paul, S.; Konar, A.)
Abstract	Sequence alignment is the procedure of comparing two (pair-wise alignment) or more (multiple sequence alignment) sequences by searching for a series of individual characters or character patterns that are in the same order in the sequences. Classical methods like Needleman-Wunsch (for global alignment) and Smith-Waterman (for local alignment) suffer from the drawback that it involves a large number of computational steps and has to statically allocate a large section of memory for computer implementation. Moreover the PAM matrix used as a scoring scheme for sequence comparison is unsuitable when we are considering only a few of the total 20 amino acids. In this paper, we propose alternate methods to obtain global and local alignment between two sequences using direct comparison and compare the performance of our algorithms with that of the classical method. We also propose an alternate scoring scheme based on fuzzy concept and discuss its advantage over conventional PAM matrix.
Sponsorship	Univ. of Melbourne Faculty of Eng
Starting Page	485
Ending Page	490
File Size	1107652
Page Count	6
File Format	PDF
ISBN	0780388402
DOI	10.1109/ICISIP.2005.1529503
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-01-04
Publisher Place	India
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Degradation Algorithm design and analysis Proteins Sequences Databases Heuristic algorithms DNA Amino acids Dynamic programming Electronic mail
Content Type	Text
Resource Type	Article

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