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P053 - GCB 2004 - German Conference on Bioinformatics

https://dl.gi.de/handle/20.500.12116/28649
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Auflistung P053 - GCB 2004 - German Conference on Bioinformatics nach Erscheinungsdatum

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  • Konferenzbeitrag
    Weighted sequencing from compomers: DNA de-novo sequencing from mass spectrometry data in the presence of false negative peaks
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Böcker, Sebastian
    One of the main endeavors in today's Life Science remains the efficient sequencing of long DNA molecules. Today, most de-novo sequencing of DNA is still performed using electrophoresis-based Sanger Sequencing introduced in 1977, in spite of certain restrictions of this method. Recently, we proposed a new method for DNA sequencing using base-specific cleavage and mass spectrometry, that appears to be a promising alternative to classical DNA sequencing approaches: Among its benefits is the extremely fast data acquisition of mass spectrometry. This leads to the combinatorial problem of Sequencing From Compomers (SFC), and to the definition of sequencing graphs. Simulations indicate that this method may allow for de-novo sequencing of DNA molecules with 200+ nt. An open problem in the context of SFC is that it does not take into account false negative peaks (missing peaks) that are common for real-world mass spectra. Here, we present a natural generalization of SFC, the Weighted Sequencing from Compomers (WSC) Problem, that allows us to cope with false negative peaks. We also show that the family of graphs introduced to solve SFC, can be generalized to capture the new aspects of WSC. Finally, we present a branch-and-bound algorithm to find all sequences that agree with the sample mass spectra with the exception of some missing peaks.
  • Konferenzbeitrag
    Identification and measurement of neigbor dependent nucleotide substitution processes
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Arndt, Peter F.
    The presence of different neighbor dependent substitution processes generates specific patterns of dinucleotide frequencies in all organisms. Based on a general framework of how to include such processes into more realistic models of nucleotide substitutions we develop a method that is able to identify such processes, measure their strength, and judge their importance to be included into the modeling. Starting from a model for neighbor independent nucleotide substitution we successively add neighbor dependent substitution processes in the order of their ability to increase the likelihood of the model describing the data. The analysis of neighbor dependent nucleotide substitutions in human, zebrafish and fruit fly is presented.
  • Konferenzbeitrag
    Conserved RNA pseudoknots
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Thurner, Caroline; Hofacker, Ivo L.; Stadler, Peter F.
    Pseudoknots are essential for the functioning of many small RNA molecules. In addition, viral RNAs often exhibit pseudoknots that are required at various stages of the viral life-cycle. Techniques for detecting evolutionarily conserved, and hence most likely functional RNA pseudoknots, are therefore of interest. Here we present an extension of the alidot approach that extracts conserved secondary structures from a multiple sequence alignment and predicted secondary structures of the individual sequences. In contrast to purely phylogenetic methods, this approach yields good results already for small samples of 10 sequences or even less.
  • Konferenzbeitrag
    Glycosciences.de: An Internet portal for glyco-related data from open access resources
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Götz, Thomas; Bohne-Lang, Andreas; Frank, Martin; Lohmann, Klaus Karl; Loss, Alexander; Lütteke, T.; Lieth, Claus-Wilhelm von der
    Carbohydrates are involved in a variety of fundamental biological processes, e.g. cellular differentiation, embryonic development or fertilization. Since glycans are secondary gene products and their structure cannot be easily predicted from DNA sequences, very little of the bioinformatics algorithm and techniques developed for genomics and proteomics research can be directly adapted for glycomics. The development of new and advanced bioinformatics tools, algorithms and data collections for glycobiology is an absolute requirement to manage and analyze successfully the large amount of data which will be produced by the upcoming glycomics project. The glycosciences.de portal aims to provide a platform, where (a) various glycorelated data collections originating from diverse open access resources as well as (b) tools helping to interpret and analyse experimental data of complex carbohydrates are made available using standard internet technologies. Access is provided based either on (sub)-structural descriptions, bibliographic data, physicochemical properties and experimental data like NMR, chemical shifts and MS-spectra. A normalised description for carbohydrate structures called LINUCS (LInear Notation for Unique description of Carbohydrate Sequences) is used to establish an efficient interchange between the implemented databases, tools and applications. The service is available at: http://www.glycosciences.de.
  • Konferenzbeitrag
    Proteochemometrics modeling of receptor-ligand interactions using rough sets
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Stömbergsson, Helena; Prusis, Peteris; Midelfart, Herman; Wikberg, Jarl E. S.; Komorowski, Jan
    We report on a model for the interaction of chimeric melanocortin G-protein coupled receptors with peptide ligands using the rough set approach. Rough sets generate If-Then rule models using Boolean reasoning. Two separate datasets have been analyzed, for which the binding affinities have previously been measured experimentally. The receptors and ligands are described by vectors of strings. Different partitions of each dataset were evaluated in order to find an optimal partition into rough set decision classes. To obtain a measurement of the accuracy of the rough set classifier generated from each dataset, a 10-fold cross validation (CV) was performed. The Area Under Curve (AUC) was calculated for each iteration during CV. This resulted in an AUC mean of 0.94 (SD 0.12) and 0.93 (SD 0.16) for the first and second dataset respectively. The CV results show that the rough set models exhibit a high classification quality. The decision rules generated from the rough set model inductions are easy to interpret. We apply this information to develop models of the interaction between ligands and receptors.
  • Konferenzbeitrag
    From composite patters to pathways – Prediction of key regulators of gene expression
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Kel, Alexander; Voss, Nico; Konovalova, Tatyana; Tchekmenev, Dmitri; Wabnitz, Philipp; Kelmargoulis, Olga; Wingender, Edgar
  • Konferenzbeitrag
    SequenceJuxtaposer: Fluid navigation for large-scale sequence comparison in context
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Slack, James; Hildebrand, Kristian; Munzner, Tamara; John, Katherine St.
    SequenceJuxtaposer is a sequence visualization tool for the exploration and comparison of biomolecular sequences. We use an information visualization technique called “accordion drawing” that guarantees three key properties: context, visibility, and frame rate. We provide context through the navigation metaphor of a rubber sheet that can be smoothly stretched to show more details in the areas of focus, while the surrounding regions of context are correspondingly shrunk. Landmarks, such as motifs or differences between aligned base pairs, are guaranteed to be visible even if located in the shrunken areas of context. Our graphics infrastructure for progressive rendering provides immediate responsiveness to user interaction by guaranteeing that we redraw the scene at a target frame rate. SequenceJuxtaposer supports interaction at 20 frames per second when browsing collections of several hundred sequences that comprise over 1.7 million total base pairs.
  • Konferenzbeitrag
    High-throughput molecular dynamics simulations: Long and short range effects of mutations on substrate specificity
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Bös, Fabian; Currle-Linde, Natalia; Lindner, Peggy; Schmid, Rolf D.; Pleiss, Jürgen
  • Konferenzbeitrag
    Probabilistic methods for predicting protein functions in protein-protein interaction networks
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Best, Christoph; Zimmer, Ralf; Apostolakis, Joannis
    We discuss probabilistic methods for predicting protein functions from protein-protein interaction networks. Previous work based on Markov Randon Fields is extended and compared to a general machine-learning theoretic approach. Using actual protein interaction networks for yeast from the MIPS database and GO-SLIM function assignments, we compare the predictions of the different probabilistic methods and of a standard support vector machine. It turns out that, with the currently available networks, the simple methods based on counting frequencies perform as well as the more sophisticated approaches.
  • Konferenzbeitrag
    Fast track to disease-specific drugs? The impact of in-situ proteomics imaging (Toponomics)
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Schubert, Walter