Randomized and parallel algorithms for distance matrix calculations in multiple sequence alignment

Journal of Clinical Monitoring and Computing

Volumn 19, Issue 4-5, 2005, Pages 351-359

  Rajasekaran, Sanguthevar ^a,e   Thapar, Vishal ^b,e   Dave, Hardik ^c   Huang, Chun Hsi ^d,e  

^a HARVARD UNIVERSITY   (United States)

^b PEC UNIVERSITY OF TECHNOLOGY   (India)

^c University of Connecticut   (United States)

^d Department of Computer Science and Engineering ^*  (United States)

^e UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Distance matrix calculation; Multiple sequence alignment; Random sampling

Indexed keywords

BIOLOGY; COMPUTATIONAL COMPLEXITY; DNA SEQUENCES; FAST FOURIER TRANSFORMS; PARALLEL ALGORITHMS; PROTEINS;

DISTANCE MATRIX CALCULATION; MULTIPLE SEQUENCE ALIGNMENT; RANDOM SAMPLING;

COMPUTATIONAL METHODS;

AMINO ACID; DNA;

ACCURACY; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CALCULATION; COMPUTER PROGRAM; DATA ANALYSIS; DNA SEQUENCE; EMPIRICISM; FOURIER TRANSFORMATION; GENETIC ALGORITHM; HUMAN; INFORMATION PROCESSING; NONHUMAN; PRIORITY JOURNAL; RANDOMIZATION; SAMPLING; SCIENTIFIC LITERATURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTING METHODOLOGIES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN;

EID: 30344444324     PISSN: 13871307     EISSN: 15732614     Source Type: Journal    
DOI: 10.1007/s10877-005-0680-3     Document Type: Article

References (20)

1. Berger MP, Munson PJ. A novel randomized iterative strategy for aligning multiple protein sequences. Computer Applications in Biosciences 1991; 7(4): 479-484. 1:CAS:528:DyaK38Xht1Chu7s%3D
2. Rajasekaran S, Nick H, Pardalos PM, Sahni S, Shaw G. Efficient algorithms for local alignment search. Journal of Combinatorial Optimization 2001; 5(1): 117-124.
3. Charter K, Schaeffer J, Szafron D. Sequence Alignment using FastLSA. International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2000: 239-245.
4. Needleman S, Wunsch C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 1970; 48: 443-453. 5420325
5. Feng D, Doolittle R. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution 1987; 25: 351-360. 3118049
6. Thompson J, Higgins D, Gibson T. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
7. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acid Res 2002; 30(14): 3059-3066. 12136088
8. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acid Res 1998; 16: 10881-10890.
9. Karypis G, Han S, Kumar V. CHAMELEON: A hierarchical clustering algorithm using dynamic modeling. Technical report TR-99. University of Minnesota, Minneapolis, 1999: 68-75.
10. Szymkowiak A, Larsen J, Hansen L. Hierarchical clustering for datamining. Fifth International Conference on Knowledge-Based Intelligent Information Engineering Systems & Allied Technologies 2001.
11. Notredame C. Recent progress in multiple sequence alignment: A survey. Pharmacogenomics 3(1): 2002.
12. Gotoh O. Furhter improvement in methods of group-to-group sequence alignment with generalized profile operations. Computer Applications in Biosciences 1994; 10(4): 379-387. 1:CAS:528:DyaK2MXht1agt7k%3D
13. Gotoh O. Optimal alignment between groups of sequences and its application to multiple sequence alignment. Computer Applications in biosciences 1993; 9(3): 361-370. 1:CAS:528:DyaK2cXnvVer
14. Kececioglu J, Lenhof H, Mehlhorn K, Mutzel P, Reinert K, Vingron M. A polyhedral approach to sequence alignment problems. Discrete applied mathematics 2000; 104: 143-186.
15. Anibal de Carvalho S. http://neobio.sourceforge.net/. Department of Computer Science, King's college, London, UK.
16. Zarembinski TI, Hung LW, et al. Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics. Proceedings of the National Academy of Science of USA 1998; 95(26): 15189-15193.
17. BLAST: http://www.ncbi.nlm.nih.gov/BLAST/Blast.cg.
18. Homo sapiens PAC clone RP5-943F2 from 7, ACCESSION AC004932 VERSION: AC004932.4 GI:13446338 http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?CMD=search&DB=nucleotide.
19. http://www.mscs.mu.edu/~cstruble/class/biin200/fall2003/notes/msa.ppt.
20. Horowitz E, Sahni S, Rajasekaran S. Computer Algorithms, WH. Freeman Press, 1998.