Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

Volumn , Issue , 2011, Pages 924-927

  Church, Philip C ^a   Goscinski, Andrzej ^a   Holt, Kathryn ^b   Inouye, Michael ^b,c   Ghoting, Amol ^d   Makarychev, Konstantin ^d   Reumann, Matthias ^e  

^a DEAKIN UNIVERSITY   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^d IBM T J WATSON RESEARCH CENTER   (United States)

^e IBM Australia   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT ALGORITHMS; BACTERIAL GENOMES; BLUE GENE; COMMODITY CLUSTERS; COMPARATIVE GENOMICS; DATA SETS; DISTRIBUTED MEMORY; GENOME SEQUENCES; LARGE DATASETS; LARGE-SCALE DATASETS; MEMORY FOOTPRINT; MULTIPLE SEQUENCE ALIGNMENT ALGORITHM; MULTIPLE SEQUENCE ALIGNMENTS; ORIGINAL ALGORITHMS;

ALIGNMENT; DATA STRUCTURES; DESIGN; GENES; SUPERCOMPUTERS;

CLUSTERING ALGORITHMS;

EID: 84055221912     PISSN: 1557170X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IEMBS.2011.6090208     Document Type: Conference Paper

References (8)

1. A. Ghoting and K. Makarychev, "Indexing genomic sequences on the IBM Blue Gene," Supercomputing 2009
2. M. A. Larkin, et al., "Clustal W and Clustal X version 2.0," Bioinformatics, vol. 23, pp. 2947-2948, November 1, 2007 2007.
3. R. C. Edgar, "MUSCLE: multiple sequence alignment with high accuracy and high throughput," Nucleic Acids Research, vol. 32, pp. 1792-1797, March 1, 2004 2004.
4. C. Notredame, et al., "T-coffee: a novel method for fast and accurate multiple sequence alignment," Journal of Molecular Biology, vol. 302, pp. 205-217, 2000.
5. A. E. Darling, et al., "progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement," PLoS One, vol. 5, p. e11147, 2010.
6. B. Ma, et al., "PatternHunter: faster and more sensitive homology search," Bioinformatics, vol. 18, pp. 440-445, 2002.
7. C. Sosa, B. Knudson. "IBM System Blue Genen Solution: Blue Gene/P Applicatino Development." 4th edition. IBM Redbooks. Sept 2009.
8. S. V. Anguoli and S. L. Salzberg. "Mugsy: fast multiple alignment of closely related whole genomes." Bioinformatics vol 27(3) pp. 334-342, 2011