By Pavel A. Pevzner (auth.), Raffaele Giancarlo, Sridhar Hannenhalli (eds.)
This booklet constitutes the refereed complaints of the seventh foreign Workshop on Algorithms in Bioinformatics, WABI 2007, held in Philadelphia, PA, united states in September 2007.
The 38 revised complete papers offered including the summary of a keynote speak have been conscientiously reviewed and chosen from 133 submissions. All present problems with algorithms in bioinformatics are addressed, starting from mathematical instruments to experimental reviews of approximation algorithms and stories on major computational analyses. quite a few organic difficulties are handled, together with genetic mapping, series alignment and series research, phylogeny, comparative genomics, and protein constitution. moreover the papers characteristic high-performance computing ways to computationally not easy studying and optimization difficulties in bioinformatics and canopy tools, software program and dataset repositories for improvement and checking out of such algorithms and their underlying models.
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Additional info for Algorithms in Bioinformatics: 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007. Proceedings
Early work by Hubbard  has been followed by other studies directed towards understanding and predicting β-sheet topology [23, 8, 26, 25, 22, 20, 15]. In a recent work, Cheng and Baldi  addressed the strand pairing problem using a three-stage approach. In the ﬁrst stage they compute, for the input protein sequence, the scores (estimated probabilities) of residue pairs as potential partners in a βstrand pairing. This computation is performed by a neural network with input describing a window of size ﬁve around each residue and the information about the distance between the two residues in the protein sequence.
Mol. Biol. : The abundance of short proteins in the mammalian proteome. : Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold. Proc. Int. Conf. Intell. Syst. Mol. Biol. : The universal protein resource (uniprot): an expanding universe of protein information. Nucleic Acids Res. : Motif Extraction and Protein Classiﬁcation. In: IEEE Computational Systems Bioinformatics Conference (CSB’05), pp. 80–85. : Svm-prot: Web-based support vector machine software for functional classiﬁcation of a protein from its primary sequence.
E. to determine the three-dimensional (3D) structure (tertiary structure) of proteins from their one-dimensional chain of amino acidic residues (primary structure) . Predicting the tertiary structure of a protein directly from its primary structure is a complex problem. A typical alternative approach is to identify a set of sub-problems, such as the prediction R. Giancarlo and S. ): WABI 2007, LNBI 4645, pp. 25–37, 2007. c Springer-Verlag Berlin Heidelberg 2007 26 M. Vassura et al. of protein secondary structures, solvent accessibility and/or prediction of residue contacts and try to search speciﬁc solutions.