PARALLEL–TCOFFEE: A PARALLEL MULTIPLE SEQUENCE ALIGNER

20th International Conference on Parallel and Distributed Computing Systems, PDCS 2007

Volumn , Issue , 2007, Pages 248-253

  Zola, Jaroslaw ^a   Yang, Xiao ^a   Rospondek, Adrian ^b   Aluru, Srinivas ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b CZESTOCHOWA UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

MESSAGE PASSING;

ALIGNERS; LIBRARY GENERATION; MESSAGE PASSING PARADIGMS; MULTIPLE SEQUENCE ALIGNMENTS; PARALLEL IMPLEMENTATIONS; PARALLEL MULTIPLE SEQUENCE; PROGRESSIVE ALIGNMENT; SEQUENTIAL PROGRAMS; SOFTWARE SUPPORT; T COFFEES;

ALIGNMENT;

EID: 84925520830     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (22)

1. Edgar, R., Batzoglou, S.: Multiple sequence alignment. Current Opinion in Structural Biology 16 (2006) 368–373
2. Notredame, C.: Recent progress in multiple sequence alignment: A survey. Pharmacogenomics 3(1) (2002) 131–144
3. Thompson, J., et al.: Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol. 314(4) (2001) 937–951
4. Elias, I.: Settling the intractability of multiple alignment. In: Proc. of ISAAC 2003. Volume 2906 of LNCS. (2003) 352–363
5. Do, C., et al.: ProbCons: Probabilistic consistency–based multiple sequence alignment. Genome Res. 15(2) (2005) 330–340
6. Notredame, C., Higgins, D., Heringa, J.: T–Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302(1) (2000) 205–217
7. Schwartz, A., Pachter, L.: Multiple alignment by sequence annealing. In: Proc. of ECCB 2006. (2006)
8. Notredame, C., Holm, L., Higgins, D.: COFFEE: an objective function for multiple sequence alignments. Bioinformatics 14(5) (1998) 407–422
9. Chenna, R., et al.: Multiple sequence alignment with the Clustal series of programs. Nuc. Acids Res. 31(13) (2003) 3497–3500
10. Gotoh, O.: Consistency of optimal sequence alignments. Bull. Math. Biol. 52(4) (1990) 509–525
11. O’Sullivan, O., et al.: 3DCoffee: Combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 340(2) (2004) 385–395
12. Saitou, N., Nei, M.: The neighbor–joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4(4) (1987) 406–425
13. Gotoh, O.: An improved algorithm for matching biological sequences. J. Mol. Biol. 162(3) (1982) 705–708
14. RCSB: Protein data bank. http://www.rcsb.org/ (2007) (last visited).
15. Polychronopoulos, C., Kuck, D.: Guided self–scheduling: A practical scheduling scheme for parallel supercomputers. IEEE Trans. on Computers 36(12) (1997) 1425–1439
16. Parmentier, G., Trystram, D., Zola, J.: Large scale multiple sequence alignment with simultaneous phylogeny inference. J. Par. Dist. Comp. 66(12) (2006) 1534–1545
17. Jiang, W., et al.: High performance MPI–2 one–sided communication over InfiniBand. In: Proc. of IEEE CCGrid 2004. (2004) 531–537
18. Kwok, Y.K., Ahmad, I.: Benchmarking and comparison of the task graph scheduling algorithms. J. Par. Dist. Comp. 59(3) (1999) 381–422
19. Bateman, A., et al.: The Pfam protein families database. Nuc. Acids Res. 32 (2004) D138–D141
20. Colles, D.: Review of Phylogenetics: the theory and practice of phylogenetic systematics. Systematic Zoology 31(1) (1982) 100–104
21. Aluru, S., Futamura, N., Mehrotra, K.: Parallel biological sequence comparison using prefix computations. J. Par. Dist. Comp. 63 (2003) 264–272
22. Wallace, I., O’Sullivan, O., Higgins, D.: Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics 21(8) (2005) 1408–1414