Get Algorithms in Bioinformatics: 7th International Workshop, PDF

By Pavel A. Pevzner (auth.), Raffaele Giancarlo, Sridhar Hannenhalli (eds.)

ISBN-10: 3540741259

ISBN-13: 9783540741251

This e-book constitutes the refereed complaints of the seventh overseas Workshop on Algorithms in Bioinformatics, WABI 2007, held in Philadelphia, PA, united states in September 2007.

The 38 revised complete papers provided 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 stories 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. additionally the papers function high-performance computing ways to computationally challenging studying and optimization difficulties in bioinformatics and canopy tools, software program and dataset repositories for improvement and trying 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

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In: Proceedings of RECOMB, pp. : Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. : An improved hidden markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. : Predicting protein quaternary structure by pseudo amino acid composition. : An introduction to variable and feature selection. : The gene ontology annotation (goa) database–an integrated resource of go annotations to the uniprot knowledgebase.

Typical values of t considered in literature vary between 7 and 12 Å. As we showed in [10], higher threshold values allow better reconstruction, and in this work we adopt t = 12 Å. An introduction to reconstruction of protein structures from contact maps can be found in [3]. To measure the similarity between two 3D protein structures, described by some set of coordinates C, C ∈ R3×n , we use the Root Mean Square Deviation (RMSD); it is defined as the smallest distance Dk = n1 ni=1 (C [i] − Ck [i])2 , where C k ∈ R3×n is obtained by rotating and translating the coordinates set C.

28 M. Vassura et al. 1 Description of COMAR and FT-COMAR COMAR (Contact Map Reconstruction) finds a set of 3D coordinates consistent with some native contact maps [10]. COMAR consists of two phases (see the pseudo code below). In the first phase it generates an initial set of 3D coordinates C ∈ R3×n while in the second phase it refines iteratively the set of coordinates by applying a correction/perturbation procedure to C. The refinement applies until the set of coordinates is consistent with the given contact map or until a control parameter becomes 0.

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Algorithms in Bioinformatics: 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007. Proceedings by Pavel A. Pevzner (auth.), Raffaele Giancarlo, Sridhar Hannenhalli (eds.)


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