396 research outputs found
Front Matter, Table of Contents, Preface, List of Authors
No full textFront Matter, Table of Contents, Preface, List of Author
Vaquita: Fast and Accurate Identification of Structural Variation Using Combined Evidence
No full textMotivation: Comprehensive identification of structural variations (SVs) is a crucial task for studying genetic diversity and diseases. However, it remains challenging. There is only a marginal consensus between different methods, and our understanding of SVs is substantially limited.In general, integration of multiple pieces of evidence including split-read, read-pair, soft-clip, and read-depth yields the best result regarding accuracy. However, doing this step by step is usually cumbersome and computationally expensive.
Result: We present Vaquita, an accurate and fast tool for the identification of structural variations, which leverages all four types of evidence in a single program. After merging SVs from split-reads and discordant read-pairs, Vaquita realigns the soft-clipped reads to the selected regions using a fast bit-vector algorithm. Furthermore, it also considers the discrepancy of depth distribution around breakpoints using Kullback-Leibler divergence. Finally, Vaquita provides an additional metric for candidate selection based on voting, and also provides robust prioritization based on rank aggregation. We show that Vaquita is robust in terms of sequencing coverage, insertion size of the library, and read length, and is comparable or even better for the identification of deletions, inversions, duplications, and translocations than state-of-the-art tools, using both simulated and real datasets. In addition, Vaquita is more than eight times faster than any other tools in comparison.
Availability: Vaquita is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and can be downloaded at http://github.com/seqan/vaquit
An iterative method for faster sum-of-pairs multiple sequence alignment
No full textReinert K, Stoye J, Will T. An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinformatics. 2000;16(9):808-814
05471 Abstract Collection – Computational Proteomics
No full textFrom 20.11.05 to 25.11.05, the Dagstuhl Seminar 05471 ``Computational Proteomics''
was held in the International Conference and Research Center (IBFI),
Schloss Dagstuhl.
During the seminar, several participants presented their current
research, and ongoing work and open problems were discussed. Abstracts of
the presentations given during the seminar as well as abstracts of
seminar results and ideas are put together in this paper. The first section
describes the seminar topics and goals in general.
Links to extended abstracts or full papers are provided, if available
05471 Executive Summary – Computational Proteomics
No full textThe Dagstuhl Seminar on Computational Proteomics brought together researchers from computer science and from proteomics to discuss the state of the art and future developments at the interface between experiment and theory. This interdisciplinary exchange covered a wide range of topics, from new experimental methods resulting in more complex data we will have to expect in the future to purely theoretical studies of what level of experimental accuracy is required in order to solve certain problems. A particular focus was also on the application side, where the participants discussed more complex experimental methodologies that are enabled by more sophisticated computational techniques. Quantitative aspects of protein expression analysis as well as posttranslational modifications in the context of disease development and diagnosis were discussed. The seminar sparked a number of new ideas and collaborations and resulted in joint grant applications and publications
08101 Abstracts Collection – Computational Proteomics
No full textThe second Dagstuhl Seminar on emph{Computational Proteomics} took place
from March 3rd to 7th, 2008 in Schloss Dagstuhl--Leibniz Center for
Informatics. This highly international meeting brought together researchers
from computer science and from proteomics to discuss the state of the art
and future developments at the interface between experiment and theory.
This interdisciplinary exchange covered a wide range of topics, from new
experimental methods resulting in more complex data we will have to expect
in the future to purely theoretical studies of what level of experimental
accuracy is required in order to solve certain problems. A particular focus
was also on the application side, where the participants discussed more
complex experimental methodologies that are enabled by more sophisticated
computational techniques. Quantitative aspects of protein expression
analysis as well as posttranslational modifications in the context of
disease development and diagnosis were discussed. The seminar sparked a
number of new ideas and collaborations and has resulted in several joint
grant applications and paper submissions.
This paper describes the seminar topics, its goals and results. The
executive summary is followed by the abstracts of the presentations given.
Links to extended abstracts or full papers are provided, if available
Next Generation Sequencing (Dagstuhl Seminar 16351)
No full textNext Generation Sequencing (NGS) data have begun to appear in many applications that are clinically relevant, such as resequencing of cancer patients, disease-gene discovery and diagnostics for rare diseases, microbiome analyses, and gene expression profiling. The analysis of sequencing data is demanding because of the enormous data volume and the need for fast turnaround time, accuracy, reproducibility, and data security. This Dagstuhl Seminar aimed at a free and deep exchange of ideas and needs between the communities of algorithmicists and theoreticians and practitioners from the biomedical field. It identified several relevant fields such as data structures and algorithms for large data sets, hardware acceleration, new problems in the upcoming age of genomes, etc. which were discussed in breakout groups
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences
No full textBackground The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson–Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software. Results We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. Conclusions With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases
Textile and Clothing Safeguards: from the ATC to the Future
No full textThe Agreement on Textiles and Clothing established the textile and clothing safeguards regime from 1995 to 2004. The current safeguards regime for these products is defined in terms of the Agreement on Safeguards, the China Textile Safeguards, and the China Product-specific Safeguards. This article examines each of these three current safeguard options and assesses them in terms of a number of relevant dimensions. It also reviews safeguard actions to date to provide a sense of continued managed trade in this area.managed trade, protectionism, safeguards, textiles and clothing, International Relations/Trade,
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