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Sequence Analysis


Sequence analysis
Alternative Transcription Start Sites: Core Promoters and Spatiotemporal Regulatory Signatures
Elizabeth Rach, Uwe Ohler
Duke University, United States

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Sequence analysis
Improved and automated residue function determination from multiple sequence alignment
Kai Ye, Gert Vriend, Adriaan IJzerman
Leiden University, Netherlands

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Sequence analysis
VAMSAS: Bridging the gaps between the analysis of DNA, Protein Sequences and Protein Structure
Jim Procter, Andrew Waterhouse, Pierre Marguerite, Dominik Lindner, Iain Milne, Tom Oldfield, Kim Henrick, Frank Wright, David Marshall, David Martin, Geoff Barton
University of Dundee, United Kingdom

Visualization and Analysis of Molecular Sequences and Structures (VAMSAS) is an extensible mechanism for storing and dynamically exchanging sequences, alignments, trees and structures between three freely available interactive graphical applications: TOPALi, Jalview and AstexViewer@MSD-EBI.

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Sequence analysis
Multiple alignment and structure prediction of non-coding RNAs
Stinus Lindgreen, Paul Gardner, Anders Krogh
University of Copenhagen, Denmark

We present a novel approach to the problem of simultaneous alignment and structure prediction for multiple RNA sequences. Using simulated annealing and a scoring system combining covariation, basepair probabilities and the log-likelihood of the alignment, we sample alignments and structure for unaligned sequences. We compare our results to other programs.

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Sequence analysis
Synchronization Properties of Protein Binding Sites
Pavol Hanus
TU München, Germany

Protein-DNA and protein-RNA binding sites recognition often corresponds to sequence specific one-dimensional diffusion. Techniques to study a similar problem of frame synchronization in communications engineering are adopted to the biological scenario and used to study the synchronization properties of different binding sites (promoters, splice sites, etc.).

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