Algorithms in Bioinformatics: 10th International Workshop, by Yelena Frid, Dan Gusfield (auth.), Vincent Moulton, Mona

By Yelena Frid, Dan Gusfield (auth.), Vincent Moulton, Mona Singh (eds.)

This publication constitutes the refereed complaints of the tenth foreign Workshop on Algorithms in Bioinformatics, WABI 2010, held in Liverpool, united kingdom, in September 2010. The 30 revised complete papers provided have been conscientiously reviewed and chosen from eighty three submissions. The papers are equipped in topical sections on biomolecular constitution: RNA, protein and molecular comparability; comparative genomics; haplotype and genotype research; high-throughput information research: subsequent new release sequencing and movement cytometry; networks; phylogenetics; and sequences, strings and motifs.

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Extra info for Algorithms in Bioinformatics: 10th International Workshop, WABI 2010, Liverpool, UK, September 6-8, 2010. Proceedings

Example text

E. some i needs to be considered in the recursion (for all j) only if it is a candidate, because otherwise it is dominated by a candidate that yields a better score. Lemma 1 (R&G sparsification). Let i2 be dominated by i1 with respect to some (i, j , dj ,j ). Then for all j it holds score (i, j , i1 , j) ≤ score (i, j , i2 , j). Proof. We start with the inequality of Def. 1 and add W (i2 + 1, j − dj ,j ) on both sides. Then the claim follows immediately from W (i1 + 1, j − dj ,j ) ≤ W (i1 + 1, i2 ) + W (i2 + 1, j − dj ,j ).

Rf ree are competitive with other approaches that construct multiple-conformer representations [24,5,6]. 5˚ A) the ensemble is not able to significantly 3 improve upon the fit-to-data (Table 1, PDB Rf ree <= Rfens ree ) . It is possible that the truly variable conformers themselves cluster into a small number of sets. This may be especially true for structures 3di9 and 1ew4, where the larger number of observations might have a bearing on the larger size of the ensemble. Moreover, for low resolutions, it is interesting to note that most of the variability observed is due to noise– less than 8 alternate conformers are truly variable in most cases.

Protein conformational flexibility analysis with noisy data. Journal of Computational Biology 15, 813–828 (2008) 21. : Study of protein dynamics by x-ray diffraction. Methods in Enzymology 131, 389–433 (1986) 22. : Chaintweak: Sampling from the neighbourhood of a protein conformation. In: Pacific Symposium on Biocomputing, pp. 52–63 (2005) 23. : Role of n-terminal site of ubc9 in sumo-1,-2, and -3 binding and conjugation. Biochemistry 42, 9959–9969 (2003) 24. : Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models.

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