NDLI: Near optimal multiple sequence alignments using a traveling salesman problem approach

Content Provider	IEEE Xplore Digital Library
Author	Korostensky, C. Gonnet, G.
Copyright Year	1999
Description	Author affiliation: Inst. of Sci. Comput., Fed. Inst. of Technol., Zurich, Switzerland (Korostensky, C.)
Abstract	We present a new method for the calculation of multiple sequence alignments (MSAs). The input to our problem are n protein sequences. We assume that the sequences are related with each other and that there exists some unknown evolutionary tree that corresponds to the MSA. One advantage of our method is that the scoring can be done with reference to this phylogenetic tree, even though the tree structure itself may remain unknown. Instead of computing an evolutionary tree, we only need to compute a circular tour of the tree which is determined via a traveling salesman problem (TSP) algorithm. Our algorithm can calculate a near optimal MSA and has a performance guarantee of n-1/n.opt (where opt is the optimal score of the MSA). The algorithm runs in O(k/sup 2/n/sup 2/) time, where k is the length of the longest input sequence. From there, we improve the alignment further. Experimental results are shown at the end.
Starting Page	105
Ending Page	114
File Size	212101
Page Count	10
File Format	PDF
ISBN	0769502687
DOI	10.1109/SPIRE.1999.796584
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	1999-09-24
Publisher Place	Mexico
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Traveling salesman problems Sequences Optimized production technology Scientific computing Proteins Tree data structures Biology computing Computational biology Amino acids DNA
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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