Algorithms

Algorithms in Bioinformatics: 9th International Workshop, by Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi PDF

By Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi (auth.), Steven L. Salzberg, Tandy Warnow (eds.)

ISBN-10: 3642042406

ISBN-13: 9783642042409

ISBN-10: 3642042414

ISBN-13: 9783642042416

These lawsuits include papers from the 2009 Workshop on Algorithms in Bioinformatics (WABI), held on the collage of Pennsylvania in Philadelphia, Pennsylvania in the course of September 12–13, 2009. WABI 2009 was once the 9th annual convention during this sequence, which makes a speciality of novel algorithms that deal with imp- tantproblemsingenomics,molecularbiology,andevolution.Theconference- phasizes study that describes computationally e?cient algorithms and information constructions which have been carried out and established in simulations and on actual facts. WABI is subsidized by means of the ecu organization for Theoretical C- puter technological know-how (EATCS) and the foreign Society for Computational Bi- ogy (ISCB). WABI 2009 used to be supported by way of the Penn Genome Frontiers Institute and the Penn heart for Bioinformatics on the collage of Pennsylvania. For the 2009 convention, ninety complete papers have been submitted for evaluate by means of this system Committee, and from this robust ?eld of submissions, 34 papers have been selected for presentation on the convention and e-book within the lawsuits. The ?nal programcovered quite a lot of themes together with gene interplay n- works, molecular phylogeny, RNA and protein constitution, and genome evolution.

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Additional resources for Algorithms in Bioinformatics: 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings

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Prediction of hybridization and melting for double-stranded nucleic acids. Biophysical Journal 87, 215–226 (2004) 13. : Thermodynamic analysis of interacting nucleic acid strands. SIAM Review 49(1), 65–88 (2007) 14. : A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry 24(13), 1664–1677 (2003) 15. : Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J. 23, 396–405 (2004) 16.

To assess the performance of biRNA, we compared its predictions with those of RNAup for 21 bacterial sRNA-mRNA pairs studied in the literature. The results are presented in 34 H. Chitsaz, R. C. Sahinalp Table 1. As it was expected, biRNA outperforms RNAup for those RNA pairs that have multiple binding sites such as OxyS-fhlA and CopA-CopT. Moreover, biRNA performs slightly better than RNAup for those pairs that have only one binding site because biRNA accounts for intramolecular as well as intermolecular base pairing in the binding sites.

A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285, 2053–2068 (1999) 38. : Secondary structures of Escherichia coli antisense micF RNA, the 5’-end of the target ompF mRNA, and the RNA/RNA duplex. Biochemistry 34, 3621–3631 (1995) 39. : A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosomebinding sites. Genes Dev. 21, 2804–2817 (2007) 40. : An expanding universe of noncoding RNAs. Science 296(5571), 1260–1263 (2002) 41.

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Algorithms in Bioinformatics: 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings by Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi (auth.), Steven L. Salzberg, Tandy Warnow (eds.)


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