Tytuł artykułu
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Warianty tytułu
Języki publikacji
Abstrakty
Multiple sequence alignment is by far the most common task in computational biology. At the same time it is very computationally demanding optimisation problem. In this paper we describe a new Grid environment designed to facilitate access to the parallel multiple sequence alignment software. Our user-oriented Grid interface provides a uniform access to several popular alignment packages like, for example, ClustalW-MPI or Parallel PhyloBuilder, and it allows large alignment instances to be solved in parallel efficiently.
Słowa kluczowe
Rocznik
Tom
Strony
33--42
Opis fizyczny
Bibliogr. 29 poz., rys., tab.
Twórcy
autor
autor
- Poznan Supercomputing and Networking Center, ul. Noskowskiego 12/14, 61-704 Poznan, Poland, piotr.dziubecki@rose.man.poznan.pl
Bibliografia
- [1] CaLi library. http://icis.pcz.pl/~zola/CaLi/, 2006.
- [2] EBI Tools. http://www.ebi.ac.uk/Tools/, 2006.
- [3] EBI Tools ClustalW Web Interface. http://www.ebi.ac.uk/clustalw, 2006.
- [4] Folding ©Home. http://folding.stanford.edu/, 2006.
- [5] Globus tookit. http://www.globus.org/toolkit/, 2006.
- [6] GridSphere project. http://www.gridsphere.org/, 2006.
- [7] TeraGrid. http://www.teragrid.org/, 2006.
- [8] Allen R, et al., Blue Gene: A vision for protein science using a petaflop supercomputer, IBM Systems /., 2001, 40(2):310-327.
- [9] Anderson D.P., Fedak G., The computational and storage potential of volunteer computing, In Proc. Of CCG 2006, 2006.
- [10] Berman R, Fox G., Hey A.J.G., eds., Grid Computing: Making The Global Infrastructure a Reality, John Wiley & Sons, 2003.
- [11] Catalyurek U., et al., A component-based implementation of multiple sequence alignment, In Proc. of the 2003 ACM Symp. on App. Comp., 2003, 122-126.
- [12] Chenna R., et al., Multiple sequence alignment with the Clustal series of programs, Nuc. Acids Res., 2003, 31(13), 3497-3500.
- [13] Clamp M., Cuff J., Searle S. M., Barton G. J., The Jalview Java alignment editor, Bioinformatics, 2004, 20, 426-427.
- [14] Cuff, J. A., Barton G. J., Application of multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins, 2000, 40(3), 502-511.
- [15] Do C .B., Mahabhashyam M. S. R, Brudno M., Batzoglou S., ProbCons: Probabilistic consistency-based multiple sequence alignment, Genome Res., 2005, 15, 330-340.
- [16] Duret L., Mouchiroud D., Gouy M., HOVERGEN, a database of homologous vertebrate genes, Nuc. Acids Res., 1994, 22, 2360-2365.
- [17] Edgar R. C., MUSCLE: Multiple sequence alignment with high accuracy and high throughput, Nuc. Acids Res., 2004, 32(5), 1792-1797.
- [18] Elmorth E., Nylen M., Oscarsson R., A user-centric cluster and grid computing portal, In Proc. of ICPP 2005, 2005.
- [19] Siebenlist R, Welch V., Grid security: The Globus perspective, In Proc. of Globus WORLD 2005.
- [20] Foster L., Globus toolkit version 4: Software for service-oriented systems, In Proc. of IFIP 2005, 2005, volume 3779 of LNCS, pages 2-13.
- [21] Hillis D. M., Moritz C, Mable B. K., eds., Molecular Systematics, chapter Phylogenetic Inference, Sinauer Associates, Inc., 1996.
- [22] Javahery H., Seffah A., Radhakrishnan T., Beyond power: Making bioinformatics tools user-centered, Comm. ACM, 2004,47(11), 58-63.
- [23] Li K. B., Clustal W-MPI: Clustal W analysis using distributed and parallel computing, Bioinformatics, 2003, 19(12), 1585-1586.
- [24] Luo J., Ahmad I., Ahmed M., Paul R., Parallel multiple sequence alignment with dynamic scheduling, In Proc. of ITCC 2005, 2005, 8-13.
- [25] Novotny J., Tuecke S., Welch V., An online credential repository for the Grid: My Proxy, In Proc. of HPDC 2001, 2001.
- [26] Parmentier G., Trystram D., Zola J., Large scale multiple sequence alignment with simultaneous phylogeny inference, / Par. Dist. Comput., 2006 (In press).
- [27] Stamatakis A., Ludwig T., Meier H., Parallel inference of a 10.000-taxon phylogeny with maximum likelihood, In Proc. of Euro-Par 2004, 2004, volume 3149 of LNCS, 997-1004.
- [28] Trystram D., Zola J., Parallel multiple sequence alignment with decentralized cache support, In Proc. of Euro-Par 2005, 2005, volume 3648 of LNCS, 1217-1226.
- [29] Welch V. et al., Security for grid services, In Proc. of IEEE Symp. HPDC, 2003, 48-57.
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BPC1-0001-0043