The following information was submitted:
Transactions: INTERNATIONAL JOURNAL of COMPUTERS
Transactions ID Number: 20-412
Full Name: Gamil Abdel-azim
Position: Associate Professor
Age: ON
Sex: Male
Address: Qassim University, Computer college, Buraydah, Qassim
Country: SAUDI ARABIA
Tel: 00966509781525
Tel prefix:
Fax:
E-mail address: gazim3@gmail.com
Other E-mails: abdaladiem@qu.edu.sa
Title of the Paper: modified progressive strategy for multiple proteins sequence alignment
Authors as they appear in the Paper: Gamil Abdel-Azim, Mohamed Ben Othman, Zaher Abo-Eleneen
Email addresses of all the authors: gazim3@gmail.com, mtothman@gmail.com, zaher_aboeleneen@yahoo.com
Number of paper pages: 11
Abstract: One of the important research topics of bioinformatics is the Multiple proteins sequence alignment. Since the exact methods for MSA have exponential time complexity, the heuristic approaches and the progressive alignment are the most commonly used in multiple sequences alignments. In this paper, we propose a modified progressive alignment strategy. Choosing and merging the most closely sequences is one of the important steps of the progressive alignment strategy. This depends on the similarity between the sequences. To measure that similarity we need to define a distance. In this paper, we construct a distance matrix. The elements of a row of this matrix correspond to the distance between a sequence to other sequences. A guide tree is built using the distance matrix. For each sequence we define a descriptor which is called also feature vector. The elements of the distance matrix are calculated based on the distance between the descriptors of the sequences. The d!
escriptor reduces the dimension of the sequence then yields to a faster calculation of distance matrix and also to obtain preliminary distance matrix without pairwise alignment in the first step. The principle contribution in this paper is the modification of the first step of the basic progressive alignment strategy ie the computation of the distance matrix which yields to a new guide tree. Such guide tree is simple to implement and gives good result's performance. A comparison between the results got from the proposed strategy and from the ClastalW over the database BAliBASE 3.0 is analyzed and reported. The Results of our testing in all dataset show that the proposed strategy is as good as Clustalw in most cases.
Keywords: Proteins sequences; Alignment; Progressive methods; Sequence descriptor; Computational molecular biology
EXTENSION of the file: .doc
Special (Invited) Session: Multiple Proteins Sequence Alignment Based on Progressive Methods with New Guide Tree
Organizer of the Session: 500-331
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